1 2 /** cf. afni_history.h **/ 3 4 #include "afni_history.h" 5 6 /* (for starting a new file, search for CHANGE) 7 8 basic format: 3-field date, user, program_name, impact_level, 9 short description without newline 10 (optional) long description with intermediate newlines 11 12 copy entire section: { ... } , 13 14 Notes: - months are JAN ... DEC (see afni_history.h) 15 16 - levels are : 17 MICRO - users don't see 18 MINOR - small effect on users 19 MAJOR - larger effect on users 20 SUPER - important changes, like new programs 21 SUPERDUPER - we expect users to know 22 23 - types are: 24 TYPE_GENERAL - unspecified update type 25 TYPE_NEW_PROG - new program 26 TYPE_NEW_OPT - new program option 27 TYPE_NEW_ENV - new environment variable or change 28 TYPE_BUG_FIX - bug fix 29 TYPE_MODIFY - a change (not new, not a fix) 30 TYPE_ENHANCE - general improvement 31 TYPE_REMOVE - deleted 32 TYPE_REINSTATE - un-deleted 33 34 - PLEASE, stick to what fits on an 80 column terminal 35 - it may be nice to put the newest entries at the top 36 - leave the last "99, NULL" entry as it is 37 38 -- examples (newest at top) -- 39 40 { 26 , FEB , 2008 , RCR , "my_program" , MAJOR , TYPE_GENERAL , 41 "short description of change" , 42 "(optional) detailed description, or where to get more information\n" 43 " - with newlines, if you babble for multiple lines\n" 44 " (but none at the end)" 45 } , 46 47 { 26, MAR, 2008, RCR, "sample", MICRO, TYPE_GENERAL, 48 "blah", 49 NULL 50 } , 51 52 */ 53 54 afni_history_struct rickr_history[] = { 55 56 { 19, Dec, 2021, RCR, "afni-general", MINOR, TYPE_MODIFY, 57 "misc updates for circleCI build based on xcode 12.4.0", 58 "Remove thd_incorrelate.o from cmake libmri, etc." 59 } , 60 61 { 19, Dec, 2021, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 62 "add -show_distmat", 63 "Display nrows x nrows matrix of distances between all vector row pairs.\n" 64 "Option added for jkblujus (AFNI MB)." 65 } , 66 67 { 9, Dec, 2021, RCR, "3dinfo", MINOR, TYPE_MODIFY, 68 "further restrict -same_center", 69 "Change def limit from 0.1*sum_vox_diags to 0.001*ave_vox_diag." 70 } , 71 72 { 9, Dec, 2021, RCR, "3dmaskdump", MINOR, TYPE_BUG_FIX, 73 "balls were not verified to be entirely within dset bounds", 74 "Thanks to aclyn11 (AFNI MB) for noting the problem." 75 } , 76 77 { 3, Dec, 2021, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 78 "add -combine_method m_tedana_tedort", 79 "Now have MEICA group tedana methods:\n" 80 " m_tedana, m_tedana_OC, m_tedana_tedort" 81 } , 82 83 { 26, Nov, 2021, RCR, "3dGrayplot", MICRO, TYPE_BUG_FIX, 84 "cs_pv.c: xt no longer malloc'd", 85 NULL 86 } , 87 88 { 24, Nov, 2021, RCR, "afni-general", MICRO, TYPE_MODIFY, 89 "put space_to_NIFTI_code() into libmri", 90 "To satisfy the evil designs of afni_proc.py." 91 } , 92 93 { 24, Nov, 2021, RCR, "3dmaskdump", MINOR, TYPE_BUG_FIX, 94 "make boxes tight; scale radius to voxel counts", 95 "Tighten boxes and balls to not include unrequested voxels.\n" 96 "Scaling the radius allows for sub-mm voxels." 97 } , 98 99 { 21, Nov, 2021, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 100 "add updates for current tedana; add -help_tedana_files", 101 NULL 102 } , 103 104 { 17, Nov, 2021, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 105 "handle uninit and if block in debugtrace.c, suma_datasets.c", 106 NULL 107 } , 108 109 { 15, Nov, 2021, RCR, "afni-general", MINOR, TYPE_MODIFY, 110 "pull THD_nifti_process_afni_ext() out of thd_niftiread.c:THD_open_nifti()", 111 "This should have no effect.\n" 112 "It is preparation for testing the AFNI extension in NIFTI against dset." 113 } , 114 115 { 8, Nov, 2021, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 116 "add -milestones, to show interesting milestones for the program", 117 NULL 118 } , 119 120 { 8, Nov, 2021, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 121 "add -milestones", 122 NULL 123 } , 124 125 { 7, Nov, 2021, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 126 "add -regress_opts_fwhmx (for adding options to 3dFWHMx)", 127 "Added on the authority of S Torrisi." 128 } , 129 130 { 29, Oct, 2021, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 131 "on mac, check for standard R not in PATH", 132 NULL 133 } , 134 135 { 28, Oct, 2021, RCR, "1d_tool.py", MICRO, TYPE_MODIFY, 136 "remove 2-run polort 0 cormat IDENTICAL automatic warnings", 137 "Done for P Taylor, as they were getting flagged in APQC." 138 } , 139 140 { 27, Oct, 2021, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 141 "try to warn on insufficient disk space", 142 "Check if any data partition has less than 5 GB available.\n" 143 "Done to appease the mighty P Taylor." 144 } , 145 146 { 21, Oct, 2021, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 147 "allow for previously set DYLD_LIBRARY_PATH", 148 NULL 149 } , 150 151 { 20, Oct, 2021, RCR, "3dDeconvolve", MINOR, TYPE_ENHANCE, 152 "do not allocate errts/fitts on -x1D_stop", 153 NULL 154 } , 155 156 { 18, Oct, 2021, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 157 "allow user-defined ROIs/masks to be used with -mask_apply", 158 "Thank to D Picchioni for the suggestion." 159 } , 160 161 { 8, Oct, 2021, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 162 "add option -show_xmat_stype_cols", 163 "Display xmat columns for speicified -stim_* regressor classes." 164 } , 165 166 { 1, Oct, 2021, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 167 "add option -show_xmat_stim_info", 168 "Display xmat info for -stim_* regressor classes." 169 } , 170 171 { 23, Sep, 2021, RCR, "3dTshift", MICRO, TYPE_ENHANCE, 172 "update help to connect tzero to stimulus timing in 3dDeconvolve", 173 "Might want to subtract 'tzero' from stimulus event times." 174 } , 175 176 { 21, Sep, 2021, RCR, "3dTshift", MINOR, TYPE_ENHANCE, 177 "propagate toffset, if not zero", 178 NULL 179 } , 180 181 { 10, Sep, 2021, RCR, "slow_surf_clustsim.py", MICRO, TYPE_ENHANCE, 182 "add web formatting to help", 183 NULL 184 } , 185 186 { 31, Aug, 2021, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 187 "add option -gert_chan_digits, to specify num digits for channel in name", 188 NULL 189 } , 190 191 { 20, Aug, 2021, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 192 "add option -write_tsv_cols_of_interest", 193 NULL 194 } , 195 196 { 14, Aug, 2021, RCR, "coxplot", MICRO, TYPE_BUG_FIX, 197 "remove duplicate symbols zzzplt_ and zzpltr_", 198 "Done at the behest of D Glen." 199 } , 200 201 { 27, Jul, 2021, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 202 "fix typo in cubic resampling for viewer/3dresample (afni_slice.c)", 203 "Done with P Taylor." 204 } , 205 206 { 26, Jul, 2021, RCR, "3dinfo", MINOR, TYPE_NEW_OPT, 207 "add options -dcx, -dcy, -dcz, dc3", 208 "This provides the center of the volumetric grid, in DICOM coords." 209 } , 210 211 { 22, Jul, 2021, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 212 "add option -multi_durations_from_offsets", 213 "Added on the authority of W-L Tseng." 214 } , 215 216 { 16, Jul, 2021, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 217 "unindent EOF command terminator in example", 218 "Thanks to I Berteletti for noting the problem." 219 } , 220 221 { 15, Jul, 2021, RCR, "gen_ss_review_table.py", MINOR, TYPE_NEW_OPT, 222 "add -empty_is_outlier, to treat empty fields as outliers", 223 "The default reporting of blank outlier test vals is now as non-outliers.\n" 224 "Use this option to report as outliers.\n" 225 "Added for the mighty P Taylor." 226 } , 227 228 { 13, Jul, 2021, RCR, "gen_ss_review_table.py", MICRO, TYPE_BUG_FIX, 229 "fix '-separator whitespace' in the case of blank lines", 230 "Thanks to P Taylor for noting the problem." 231 } , 232 233 { 25, Jun, 2021, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 234 "add -rand_post_elist_partition", 235 "This will partition an already defined stim class into new ones.\n" 236 "Added on the authority of S Haller." 237 } , 238 239 { 22, Jun, 2021, RCR, "3dSurf2Vol", MINOR, TYPE_MODIFY, 240 "without -datum, the output now depends on the map func, not the BRIK", 241 "Done to appease the mysterious D Glen.\n" 242 } , 243 244 { 22, Jun, 2021, RCR, "suma-general", MINOR, TYPE_BUG_FIX, 245 "calm those grumpy compilers", 246 "Issues noted by P Taylor.\n" 247 } , 248 249 { 14, Jun, 2021, RCR, "dcm2niix_afni", MICRO, TYPE_BUG_FIX, 250 "turn of local signing in crorden/dcm2niix_console/makefile", 251 NULL 252 } , 253 254 { 10, Jun, 2021, RCR, "SurfLocalstat", MINOR, TYPE_NEW_PROG, 255 "add Ziad's program to the default build", 256 "This is to allow use of the 'mode' stat." 257 } , 258 259 { 10, Jun, 2021, RCR, "afni-general", MINOR, TYPE_MODIFY, 260 "rename src/suma_suma.h to src/SUMA/SUMA_X_objs.h", 261 "This is to avoid glorious case-insensitive name conflicts on Macs.\n" 262 "As suggested by the merciful D Glen." 263 } , 264 265 { 3, Jun, 2021, RCR, "dcm2niix_afni", MINOR, TYPE_ENHANCE, 266 "sync crorden/dcm2niix_console with repo, version v1.0.20210317", 267 "Thanks to C Rorden for suggesting the update." 268 } , 269 270 { 1, Jun, 2021, RCR, "afni-general", MINOR, TYPE_MODIFY, 271 "AFNI_COMPRESSOR no longer affects NIFTI (seems AFNI_AUTOGZIP never did)", 272 NULL 273 } , 274 275 { 29, May, 2021, RCR, "SurfLocalstat", MICRO, TYPE_NEW_OPT, 276 "add 'mode' stat modal smoothing", 277 NULL 278 } , 279 280 { 19, May, 2021, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 281 "fix volreg TSNR computation in surface analysis (TSNR still in volume)", 282 NULL 283 } , 284 285 { 1, May, 2021, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 286 "fix niml.dset suffix in the case of -regress_compute_fitts on the surface", 287 "Thanks to the all-seeing S Torrisi for noting the problem." 288 } , 289 290 { 6, Apr, 2021, RCR, "ap_run_simple_rest.tcsh", MAJOR, TYPE_NEW_PROG, 291 "run a quick afni_proc.py resting state analysis for QC", 292 NULL 293 } , 294 295 { 16, Mar, 2021, RCR, "afni-general", MINOR, TYPE_NEW_OPT, 296 "simplify logic in THD_mask_erode(), with negligible slowdown", 297 NULL 298 } , 299 300 { 15, Mar, 2021, RCR, "3dBrickStat", MINOR, TYPE_NEW_OPT, 301 "add convenience options -perclist and -perc_quiet", 302 NULL 303 } , 304 305 { 13, Mar, 2021, RCR, "Makefile.macos_10.12_local", MINOR, TYPE_ENHANCE, 306 "distribute libXp.6.dylib, since XQuartz has stopped doing it", 307 "Thanks to C Gaillard and others on the MB." 308 } , 309 310 { 10, Mar, 2021, RCR, "lib_tsv.py", MINOR, TYPE_NEW_PROG, 311 "new TSV class library, geared toward BIDS event files", 312 NULL 313 } , 314 315 { 8, Mar, 2021, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 316 "applying NIFTI scale_slope to dset must be after setting ADN_datum", 317 "Previously, NIFTI scalars were applied only after a DSET_load().\n" 318 "Thanks to D Glen for reporting the issue." 319 } , 320 321 { 5, Mar, 2021, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 322 "add option -show_cormat_warnings_full", 323 "This version includes the baseline terms in the warning list." 324 } , 325 326 { 4, Mar, 2021, RCR, "3dROIstats", MINOR, TYPE_BUG_FIX, 327 "fix surprising slowness", 328 "This would previously unload/mallocize/reload every time point,\n" 329 "possibly to free completed data. Then NIFTI input would be re-read\n" 330 "every time point (this might have changed due to something else).\n" 331 "Instead, mallocize in the first place, not per time point.\n" 332 "Also, avoid scaling floats by 1.0.\n" 333 "Thanks to C Craddock for reporting the problem." 334 } , 335 336 { 3, Mar, 2021, RCR, "@update.afni.binaries", MINOR, TYPE_MODIFY, 337 "update dotfiles for 'complete' files before running apsearch", 338 "Do this so apsearch will not tell users to update the dotfiles again.\n" 339 "Thanks to D Glen." 340 } , 341 342 { 3, Mar, 2021, RCR, "@clean_help_dir", MINOR, TYPE_MODIFY, 343 "warn on any error in 'cat *.complete* > xx' commands", 344 "In MacOS 11 Rosetta terminals, those commands are *sometimes* crashing.\n" 345 "Warn on any such failure.\n" 346 "Such a crash could cause trouble for other programs, too.\n" 347 "Thanks to D Glen." 348 } , 349 350 { 24, Feb, 2021, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 351 "add options -regress_extra_ortvec, -regress_extra_ortvec_labels", 352 "Pass sets of regressors of no interest, to go into the baseline.\n" 353 "Requested by multiple people, including Carolin31 on MB." 354 } , 355 356 { 22, Feb, 2021, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 357 "masking is no longer applied to TSNR dset; pass mask_dset to gen_ss", 358 "Requested by P Taylor." 359 } , 360 361 { 21, Feb, 2021, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 362 "remove actual targets in RM for LIBMRI_*", 363 NULL 364 } , 365 366 { 21, Feb, 2021, RCR, "@djunct_glue_imgs_vert", MICRO, TYPE_MODIFY, 367 "allow -help without deps, so move dependency tests", 368 NULL 369 } , 370 371 { 19, Feb, 2021, RCR, "suma-general", MINOR, TYPE_MODIFY, 372 "updates for ShowMode in SUMA_xColBar.c", 373 "Resolve compiler warnings, but avoid logic changes at the same time\n" 374 "as XQuartz beta issues. So temporarily keep original logic.\n" 375 "Once we feel stable with XQuartz, look into expected fixes.\n" 376 "Search for 'todo: apply ShowMode' in SUMA_xColBar.c." 377 } , 378 379 { 18, Feb, 2021, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 380 "warn about problematic version of XQuartz", 381 "Bad versions seem to be 2.8.0_alpa*, 2.8.0_betas[12] (3+ okay?).\n" 382 "With improvements we have seen, maybe we should warn on any beta." 383 } , 384 385 { 17, Feb, 2021, RCR, "afni-general", MINOR, TYPE_MODIFY, 386 "moved AFNI_ijk_* protos from afni.h to 3ddata.h", 387 "All thd_coords.c protos are in 3ddata.h now." 388 } , 389 390 { 26, Jan, 2021, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 391 "do not convert NIFTI scaled shorts to float", 392 "If slope!=0 && inter==0, pass slope as brick_fac.\n" 393 "Thanks to C Caballero and S Moia for reporting this." 394 } , 395 396 { 3, Jan, 2021, RCR, "SurfMeasures", MINOR, TYPE_MODIFY, 397 "shift memory allocation/free around, mostly to match libSUMA", 398 "Inspired by C Rorden via sanitizer warnings." 399 } , 400 401 { 31, Dec, 2020, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 402 "modify help: be more clear about bandpassing being undesirable", 403 "Also, add example of high-pass filter to model slow drift.\n" 404 "See help for option -regress_polort." 405 } , 406 407 { 29, Dec, 2020, RCR, "nifti_tool", MICRO, TYPE_ENHANCE, 408 "add help example for creating a new dataset given a raw data file", 409 NULL 410 } , 411 412 { 29, Dec, 2020, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 413 "sync with nifti_clib", 414 NULL 415 } , 416 417 { 22, Dec, 2020, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 418 "fixed 6 copy-and-paste errors using MRI_TYPE_maxval", 419 "Thanks to C Rorden for bringing this up and suggesting code fixes." 420 } , 421 422 { 17, Dec, 2020, RCR, "1dBport", MICRO, TYPE_BUG_FIX, 423 "guard against silent failure of int overflow for ftop", 424 NULL 425 } , 426 427 { 29, Sep, 2020, RCR, "3dANOVA3", MICRO, TYPE_ENHANCE, 428 "be specific about limits for 'param must be in' error messages", 429 NULL 430 } , 431 432 { 17, Sep, 2020, RCR, "afni_system_check.py", MINOR, TYPE_BUG_FIX, 433 "fix use of platform.mac_ver (was there a change?)", 434 NULL 435 } , 436 437 { 15, Sep, 2020, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 438 "whine if .zshrc references all_progs.COMP.bash; backup for distro", 439 NULL 440 } , 441 442 { 14, Sep, 2020, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 443 "update .zshrc: set PATH and DYLD_L_P..., and source all_progs.COMP.zsh", 444 NULL 445 } , 446 447 { 14, Sep, 2020, RCR, "apsearch", MINOR, TYPE_ENHANCE, 448 "create complete.zsh files - like bash ones, but cleaned a little", 449 NULL 450 } , 451 452 { 2, Sep, 2020, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 453 "add options -show_field and -show_field_names", 454 "Using the new -show_field option, for each entry one can show:\n" 455 " - the full entry (as before)\n" 456 " - only the first/main line\n" 457 " - only the program name, or date, or author, etc." 458 } , 459 460 { 31, Aug, 2020, RCR, "afni_python_wrapper.py", MICRO, TYPE_NEW_OPT, 461 "add -joinn for list output; add list_intersect and list_diff funcs", 462 NULL 463 } , 464 465 { 27, Aug, 2020, RCR, "SUMA_test_DrawingAreaWidget", MICRO, TYPE_ENHANCE, 466 "set up for alternatively building without SUMA", 467 NULL 468 } , 469 470 { 27, Aug, 2020, RCR, "@diff.tree", MICRO, TYPE_BUG_FIX, 471 "better handling of missing trailing directory args", 472 NULL 473 } , 474 475 { 26, Aug, 2020, RCR, "ClustExp_StatParse.py", MICRO, TYPE_ENHANCE, 476 "python 3 update to decode() subprocess output", 477 NULL 478 } , 479 480 { 26, Aug, 2020, RCR, "Makefile.INCLUDE", MINOR, TYPE_ENHANCE, 481 "much limiting of line lengths to 80 chars - should be no real change", 482 NULL 483 } , 484 485 { 25, Aug, 2020, RCR, "1dDW_Grad_o_Mat", MINOR, TYPE_REMOVE, 486 "removed from distribution - use 1dDW_Grad_o_Mat++", 487 NULL 488 } , 489 490 { 25, Aug, 2020, RCR, "3dANALYZEtoAFNI", MINOR, TYPE_REMOVE, 491 "removed from distribution - use 3dcopy or to3d", 492 NULL 493 } , 494 495 { 25, Aug, 2020, RCR, "3dAnatNudge", MINOR, TYPE_REMOVE, 496 "removed from distribution - use align_epi_anat.py", 497 NULL 498 } , 499 500 { 25, Aug, 2020, RCR, "3dCountSpikes", MINOR, TYPE_REMOVE, 501 "removed from distribution - use 3dToutcount", 502 NULL 503 } , 504 505 { 25, Aug, 2020, RCR, "3dDeconvolve_f", MINOR, TYPE_REMOVE, 506 "removed from distribution - use 3dDeconvolve", 507 NULL 508 } , 509 510 { 25, Aug, 2020, RCR, "3dFWHM", MINOR, TYPE_REMOVE, 511 "removed from distribution - use 3dFWHMx", 512 NULL 513 } , 514 515 { 25, Aug, 2020, RCR, "3dFourier", MINOR, TYPE_REMOVE, 516 "removed from distribution - use 3dBandpass", 517 NULL 518 } , 519 520 { 25, Aug, 2020, RCR, "3dMax", MINOR, TYPE_REMOVE, 521 "removed from distribution - use 3dBrickStat", 522 NULL 523 } , 524 525 { 25, Aug, 2020, RCR, "3dProbTrackID", MINOR, TYPE_REMOVE, 526 "removed from distribution - use 3dTrackID", 527 NULL 528 } , 529 530 { 25, Aug, 2020, RCR, "3dUniformize", MINOR, TYPE_REMOVE, 531 "removed from distribution - use 3dUnifize", 532 NULL 533 } , 534 535 { 25, Aug, 2020, RCR, "3dWavelets", MINOR, TYPE_REMOVE, 536 "removed from distribution", 537 NULL 538 } , 539 540 { 25, Aug, 2020, RCR, "3dbuc2fim", MINOR, TYPE_REMOVE, 541 "removed from distribution", 542 NULL 543 } , 544 545 { 25, Aug, 2020, RCR, "3ddup", MINOR, TYPE_REMOVE, 546 "removed from distribution", 547 NULL 548 } , 549 550 { 25, Aug, 2020, RCR, "3dfim", MINOR, TYPE_REMOVE, 551 "removed from distribution - use 3dDeconvolve", 552 NULL 553 } , 554 555 { 25, Aug, 2020, RCR, "3dnoise", MINOR, TYPE_REMOVE, 556 "removed from distribution", 557 NULL 558 } , 559 560 { 25, Aug, 2020, RCR, "3dproject", MINOR, TYPE_REMOVE, 561 "removed from distribution", 562 NULL 563 } , 564 565 { 25, Aug, 2020, RCR, "3dttest", MINOR, TYPE_REMOVE, 566 "removed from distribution - use 3dttest++", 567 NULL 568 } , 569 570 { 25, Aug, 2020, RCR, "AlphaSim", MINOR, TYPE_REMOVE, 571 "removed from distribution - use 3dClustSim", 572 NULL 573 } , 574 575 { 25, Aug, 2020, RCR, "Dimon1", MINOR, TYPE_REMOVE, 576 "removed from distribution - use Dimon", 577 NULL 578 } , 579 580 { 25, Aug, 2020, RCR, "FD2", MINOR, TYPE_REMOVE, 581 "removed from distribution - use afni", 582 NULL 583 } , 584 585 { 25, Aug, 2020, RCR, "Ifile", MINOR, TYPE_REMOVE, 586 "removed from distribution - use Dimon", 587 NULL 588 } , 589 590 { 25, Aug, 2020, RCR, "Xphace", MINOR, TYPE_REMOVE, 591 "removed from distribution", 592 NULL 593 } , 594 595 { 25, Aug, 2020, RCR, "abut", MINOR, TYPE_REMOVE, 596 "removed from distribution", 597 NULL 598 } , 599 600 { 25, Aug, 2020, RCR, "ent16", MINOR, TYPE_REMOVE, 601 "removed from distribution", 602 NULL 603 } , 604 605 { 25, Aug, 2020, RCR, "ftosh", MINOR, TYPE_REMOVE, 606 "removed from distribution", 607 NULL 608 } , 609 610 { 25, Aug, 2020, RCR, "ge_header", MINOR, TYPE_REMOVE, 611 "removed from distribution - use Dimon", 612 NULL 613 } , 614 615 { 25, Aug, 2020, RCR, "mayo_analyze", MINOR, TYPE_REMOVE, 616 "removed from distribution - use nifti_tool", 617 NULL 618 } , 619 620 { 25, Aug, 2020, RCR, "mritopgm", MINOR, TYPE_REMOVE, 621 "removed from distribution", 622 NULL 623 } , 624 625 { 25, Aug, 2020, RCR, "siemens_vision", MINOR, TYPE_REMOVE, 626 "removed from distribution - use Dimon", 627 NULL 628 } , 629 630 { 25, Aug, 2020, RCR, "sqwave", MINOR, TYPE_REMOVE, 631 "removed from distribution", 632 NULL 633 } , 634 635 { 25, Aug, 2020, RCR, "plug_3ddup.so", MINOR, TYPE_REMOVE, 636 "removed from distribution", 637 NULL 638 } , 639 640 { 25, Aug, 2020, RCR, "3dICC_REML.R", MINOR, TYPE_REMOVE, 641 "removed from distribution", 642 NULL 643 } , 644 645 { 25, Aug, 2020, RCR, "3dAOV.R", MINOR, TYPE_REMOVE, 646 "removed from distribution", 647 NULL 648 } , 649 650 { 25, Aug, 2020, RCR, "lpc_align.py", MINOR, TYPE_REMOVE, 651 "removed from distribution - use align_epi_anat.py", 652 NULL 653 } , 654 655 { 25, Aug, 2020, RCR, "check_dset_for_fs.py", MINOR, TYPE_REMOVE, 656 "removed from distribution", 657 NULL 658 } , 659 660 { 25, Aug, 2020, RCR, "afni_restproc.py", MINOR, TYPE_REMOVE, 661 "removed from distribution - use afni_proc.py", 662 NULL 663 } , 664 665 { 25, Aug, 2020, RCR, "DoPerRoi.py", MINOR, TYPE_REMOVE, 666 "removed from distribution", 667 NULL 668 } , 669 670 { 25, Aug, 2020, RCR, "@snapshot_volreg3", MINOR, TYPE_REMOVE, 671 "removed from distribution - use @snapshot_volreg", 672 NULL 673 } , 674 675 { 25, Aug, 2020, RCR, "@make_stim_file", MINOR, TYPE_REMOVE, 676 "removed from distribution - use timing_tool.py", 677 NULL 678 } , 679 680 { 25, Aug, 2020, RCR, "@auto_align", MINOR, TYPE_REMOVE, 681 "removed from distribution - use align_epi_anat.py", 682 NULL 683 } , 684 685 { 25, Aug, 2020, RCR, "@UpdateAfni", MINOR, TYPE_REMOVE, 686 "removed from distribution - use @update.afni_binaries", 687 NULL 688 } , 689 690 { 25, Aug, 2020, RCR, "@DTI_studio_reposition", MINOR, TYPE_REMOVE, 691 "removed from distribution", 692 NULL 693 } , 694 695 { 25, Aug, 2020, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 696 "added new types TYPE_REMOVE and TYPE_REINSTATE", 697 "This is to track when programs or notable functionality gets removed." 698 } , 699 700 { 3, Aug, 2020, RCR, "plug_vol2surf", MINOR, TYPE_BUG_FIX, 701 "fix sB update when changing surf order from 0,1 to 1,0", 702 "In only the case of setting the plugin surf_A/surf_B order to 1,0, the\n" 703 "need to update the surf_B index was not recognized, and it stayed at 1\n" 704 "(instead of the requested 0).\n" 705 "Thanks to D Glen for reporting the problem." 706 } , 707 708 { 28, Jul, 2020, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 709 "add initial afni_history_laurenpd.c", 710 NULL 711 } , 712 713 { 21, Jul, 2020, RCR, "model_conv_PRF_6", MINOR, TYPE_ENHANCE, 714 "add env var control over pre-comp e2x, limit and pieces", 715 "See AFNI_MODEL_PRF_PRECOMPUTE_EX, AFNI_MODEL_PRF_MAX_EXP and\n" 716 "AFNI_MODEL_PRF_MAX_EXP_PIECES.\n" 717 } , 718 719 { 21, Jul, 2020, RCR, "get_afni_model_PRF_6", MINOR, TYPE_ENHANCE, 720 "add initial NT parameter", 721 NULL 722 } , 723 724 { 16, Jul, 2020, RCR, "afni-general", MINOR, TYPE_ENHANCE, 725 "update for shared libmri.so: linux_centos_7_64, linux_ubuntu_16_64", 726 NULL 727 } , 728 729 { 19, Jun, 2020, RCR, "parse_fs_lt_log.py", MICRO, TYPE_ENHANCE, 730 "update for python3, though this program might not be in use", 731 NULL 732 } , 733 734 { 19, Jun, 2020, RCR, "afni_restproc.py", MICRO, TYPE_MODIFY, 735 "update for python3; add extra suggests that it is obsolete", 736 NULL 737 } , 738 739 { 1, Jun, 2020, RCR, "3dAllinate", MICRO, TYPE_MODIFY, 740 "clear any initial ntt from master", 741 NULL 742 } , 743 744 { 1, Jun, 2020, RCR, "afni-general", MINOR, TYPE_MODIFY, 745 "in populate_nifti_image(), call time series only if ntt>1 or NVALS==1", 746 "This is to avoid confusion when a time series is used to master a\n" 747 "non-time series dataset." 748 } , 749 750 { 1, Jun, 2020, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 751 "add -show_regs and -show_regs_style", 752 "Show column indices or labels of an xmat.1D file with empty (all-zero)\n" 753 "regressors. An index list can be space or comma-separeated, or encoded.\n" 754 "Example 30 shows typical use cases.\n" 755 "Added for S Haller." 756 } , 757 758 { 31, May, 2020, RCR, "@diff.files", MICRO, TYPE_NEW_OPT, 759 "add -verb", 760 NULL 761 } , 762 763 { 26, May, 2020, RCR, "@move.to.series.dirs", MICRO, TYPE_MODIFY, 764 "call afni_python_wrapper.py instead of old afni_util.py", 765 NULL 766 } , 767 768 { 25, May, 2020, RCR, "Makefile.macos_10.12_local", MINOR, TYPE_ENHANCE, 769 "add libexpat.1.dylib to EXTRA_INSTALL_FILES", 770 "R was upgraded to 3.6 (on the 10.12 build machine), since that is the\n" 771 "current G Chen version requirement, making R_io.so work for people with\n" 772 "only 3.6. But libexpat was upgraded too, which afni depends on, meaning\n" 773 "systems needed that new version of libexpat, or afni would not work.\n" 774 "Instead, libexpat.1.dylib is now simply included with the binaries.\n" 775 "Thanks to S Gotts and K Tran for reporting the problem." 776 } , 777 778 { 21, May, 2020, RCR, "3dmask_tool", MINOR, TYPE_NEW_OPT, 779 "add options -NN1, -NN2 and -NN3", 780 "Also, fix tiny origin shift when large zero-padding is applied." 781 } , 782 783 { 20, May, 2020, RCR, "3dmask_tool", MINOR, TYPE_BUG_FIX, 784 "fix history and memory loss", 785 NULL 786 } , 787 788 { 20, May, 2020, RCR, "afni-general", MINOR, TYPE_ENHANCE, 789 "update THD_mask_erode_sym() akin to take NN param", 790 "This matches the dglen update to THD_mask_dilate()." 791 } , 792 793 { 11, May, 2020, RCR, "afni-general", MINOR, TYPE_ENHANCE, 794 "update web links to help pages in uber*.py", 795 "Update uber_align_test.py, uber_skel.py, uber_subj.py and uber_ttest.py." 796 } , 797 798 { 11, May, 2020, RCR, "afni-general", MINOR, TYPE_ENHANCE, 799 "updates for python3", 800 "Update xmat_tool.py, quick.alpha.vals.py, read_matlab_files.py,\n" 801 "uber_align_test.py and uber_skel.py." 802 } , 803 804 { 4, May, 2020, RCR, "@update.afni.binaries", MINOR, TYPE_BUG_FIX, 805 "fix download of test file", 806 "Thanks to Gerome on MB for reporting the problem." 807 } , 808 809 { 4, May, 2020, RCR, "xmat_tool.py", MINOR, TYPE_ENHANCE, 810 "make partual updates for python3", 811 NULL 812 } , 813 814 { 4, May, 2020, RCR, "suma-general", MINOR, TYPE_MODIFY, 815 "remove tabs from a bunch of files", 816 NULL 817 } , 818 819 { 29, Apr, 2020, RCR, "@chauffeur_afni", MINOR, TYPE_ENHANCE, 820 "add AFNI_DRIVE_OPTS_XVFB env var for adding opts to Xvfb", 821 "This will probably be modified later, but it allows one to pass\n" 822 "something like '-nolisten inet6' if IPv6 is not working.\n" 823 "Thanks to W-L Tseng." 824 } , 825 826 { 29, Apr, 2020, RCR, "@update.afni.binaries", MINOR, TYPE_MODIFY, 827 "for recur, def to pub/dist/bin/misc; terminate on failed test download", 828 NULL 829 } , 830 831 { 23, Apr, 2020, RCR, "to3d", MICRO, TYPE_BUG_FIX, 832 "allow no controller open on input of JPEG image", 833 NULL 834 } , 835 836 { 14, Apr, 2020, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 837 "if dataset inputs had full paths, use them in proc script", 838 "Thanks to W-L Tseng for pointing out the discrepancy." 839 } , 840 841 { 7, Apr, 2020, RCR, "nifti_tool", MINOR, TYPE_NEW_OPT, 842 "add -see_also and -ver_man to help create a quick man page", 843 "To create a man page (via help2man), consider:\n" 844 " nifti_tool -see_also > nt.see_also.txt\n" 845 " help2man --help-option=-help --version-option=-ver_man \\\n" 846 " --include nt.see_also.txt --no-info nifti_tool \\\n" 847 " | gzip > nifti_tool_manpage.1.gz\n" 848 "after which one can install the file, or test via\n" 849 " man ./nifti_tool_manpage.1.gz\n" 850 "(see the uncompressed version for syntax)." 851 } , 852 853 { 31, Mar, 2020, RCR, "neuro_deconvolve.py", MINOR, TYPE_ENHANCE, 854 "update for python3", 855 NULL 856 } , 857 858 { 31, Mar, 2020, RCR, "afni_system_check.py", MICRO, TYPE_BUG_FIX, 859 "grep from $HOME/.bash_profile", 860 NULL 861 } , 862 863 { 31, Mar, 2020, RCR, "afni_system_check.py", MINOR, TYPE_BUG_FIX, 864 "fix lib_system_check:self.os_dist for newer python", 865 NULL 866 } , 867 868 { 30, Mar, 2020, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 869 "have module_test_lib.py (and so afni_proc.py) work on python 2.6 again", 870 "Done for S Horovitz." 871 } , 872 873 { 27, Mar, 2020, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 874 "PY_LIBS", 875 NULL 876 } , 877 878 { 26, Mar, 2020, RCR, "apqc_make_tcsh.py", MICRO, TYPE_MODIFY, 879 "move ohtml to lib_apqc_tcsh.py and remove import of apqc_make_html", 880 "This is in keeping with all python libs being under afnipy." 881 } , 882 883 { 24, Mar, 2020, RCR, "python_module_test.py", MINOR, TYPE_MODIFY, 884 "restore approximate previous behavior", 885 NULL 886 } , 887 888 { 23, Mar, 2020, RCR, "3drefit", MINOR, TYPE_NEW_OPT, 889 "add options -oblique_recenter and -oblique_recenter_raw", 890 "Adjust the origin so the cardinalized 0,0,0 (e.g. seen in the afni GUI)\n" 891 "is in the same brain location as it was originally (in the scanner?).\n" 892 "So when viewing an oblique volume on top of a '3dWarp -deoblique' output,\n" 893 "coordinate 0,0,0 will match between them." 894 } , 895 896 { 20, Mar, 2020, RCR, "Makefile.INCLUDE", MINOR, TYPE_MODIFY, 897 "fix PY_DIR, update PY vars, add list_py_libs", 898 NULL 899 } , 900 901 { 20, Mar, 2020, RCR, "Makefile.INCLUDE", MINOR, TYPE_MODIFY, 902 "fix PY_DIR, update PY vars, add list_py_libs", 903 NULL 904 } , 905 906 { 19, Mar, 2020, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 907 "fix use of module_test_lib.py with change to new afnipy dir", 908 NULL 909 } , 910 911 { 12, Mar, 2020, RCR, "afni-general", MINOR, TYPE_MODIFY, 912 "point web help for program to sphinx tree", 913 "Also, added -hweb/-h_web for python progs that use option_list.py." 914 } , 915 916 { 12, Mar, 2020, RCR, "SUMA_test_DrawingAreaWidget", MINOR, TYPE_NEW_PROG, 917 "test for a valid DrawingAreaWidgetClass pointer", 918 NULL 919 } , 920 921 { 12, Mar, 2020, RCR, "align_epi_anat.py", MICRO, TYPE_BUG_FIX, 922 "account for lpc+zz when checking costs for -check_flip", 923 "Thanks to R Kampe for noting the problem." 924 } , 925 926 { 11, Mar, 2020, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 927 "add details on why some help examples are not considered complete", 928 "And corrected status of Example 11, changed to recommended.\n" 929 "Thanks to K Knutson for questioning the status." 930 } , 931 932 { 5, Mar, 2020, RCR, "@SUMA_Make_Spec_FS", MINOR, TYPE_MODIFY, 933 "for now, use mris_convert/3dcopy for extra annot files", 934 "So standard mesh version will not have a proper label table, but\n" 935 "the values will be appropriate and more usable in suma.\n" 936 "This is done to import the Schaefer/Yeo atlases onto standard meshes.\n" 937 "Done with D Glen." 938 } , 939 940 { 3, Mar, 2020, RCR, "3dttest++", MICRO, TYPE_MODIFY, 941 "have 3dttest++ -Clustsim fail immediately if -prefix includes a path", 942 NULL 943 } , 944 945 { 27, Feb, 2020, RCR, "@SUMA_Make_Spec_FS", MINOR, TYPE_NEW_OPT, 946 "add -fsannot_ver; apply -extra_annot_labels output as -extra_fs_dsets", 947 NULL 948 } , 949 950 { 26, Feb, 2020, RCR, "@SUMA_AlignToExperiment", MICRO, TYPE_MODIFY, 951 "NIFTI fails for -exp_anat, so have it fail early and explain", 952 "Thanks to D Oswalt for noting the problem." 953 } , 954 955 { 19, Feb, 2020, RCR, "afni_python_wrapper.py", MAJOR, TYPE_NEW_PROG, 956 "replaces afni_util.py as a main", 957 "This program can theortically be used to call any AFNI python function\n" 958 "from the shell." 959 } , 960 961 { 19, Feb, 2020, RCR, "afni_util.py", MINOR, TYPE_MODIFY, 962 "no longer available as a main executable", 963 NULL 964 } , 965 966 { 19, Feb, 2020, RCR, "apsearch", MICRO, TYPE_MODIFY, 967 "get process depth via afni_python_wrapper.py", 968 "afni_util.py main was moved to afni_python_wrapper.py." 969 } , 970 971 { 19, Feb, 2020, RCR, "@auto_tlrc", MICRO, TYPE_BUG_FIX, 972 "block inappropriate 'FATAL ERROR: ... already exists'", 973 "This happened when anat_in was local and stripped, so it matched ns_pref.\n" 974 "Thanks to R Kampe for noting the problem." 975 } , 976 977 { 18, Feb, 2020, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 978 "help examples now include some developed outside of afni_proc.py", 979 "This includes some class demos, along with pamenc and NARPS.\n" 980 "Include a line about whether each example is reasonably recommended.\n" 981 "Done to appease the mighty P Taylor." 982 } , 983 984 { 18, Feb, 2020, RCR, "@Align_Centers", MICRO, TYPE_BUG_FIX, 985 "fix copy-and-paste erro and missing endif", 986 "Thanks to R Kampe for noting the problem." 987 } , 988 989 { 14, Feb, 2020, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 990 "add -compare_opts_vs_opts", 991 "One can compare two afni_proc.py commmands sequentially, that are\n" 992 "not part of the stored examples list. Consider:\n" 993 " afni_proc.py ... first option set ... \\\n" 994 " -compare_opts_vs_opts \\\n" 995 " ... second option set ...\n" 996 "It is okay for 'second option set' to include the afni_proc.py\n" 997 "command name, in case two scripts are concatenated." 998 } , 999 1000 { 12, Feb, 2020, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 1001 "add ability to compare against examples", 1002 "Add options -compare_opts, -compare_example_pair, -show_example and\n" 1003 " -show_example_names.\n" 1004 "Consider these examples:\n" 1005 " afni_proc.py -show_example 'Example 11b'\n" 1006 " afni_proc.py -show_example_names\n" 1007 " afni_proc.py ... my options here ... -compare_opts 'Example 11'\n" 1008 "Motivated by C Gaillard and P Taylor." 1009 } , 1010 1011 { 7, Feb, 2020, RCR, "Makefile.linux_fedora_28_shared", MINOR, TYPE_ENHANCE, 1012 "build main non-X11, non-SUMA AFNI program without X deps", 1013 "Set LLIBS_X11 to current LLIBS, and give it to SUMA_LINK_LIB.\n" 1014 "Remove all X11 libs from LLIBS. Add -DREPLACE_XT to CEXTRA.\n" 1015 "Note: without REPLACE_XT, LLIBS could still just use Xt and X11.\n" 1016 "And made the same mods to Makefile.linux_xorg7_64." 1017 } , 1018 1019 { 7, Feb, 2020, RCR, "afni-general", MINOR, TYPE_MODIFY, 1020 "reduce X11 program deps", 1021 "Possibly define LLIBS_X11 in top-level Makefile (as current LLIBS) and\n" 1022 "then remove X libs from LLIBS. M.INCLUDE will define LLIBS if not set.\n" 1023 "Move suma_help to IMOBJS." 1024 } , 1025 1026 { 5, Feb, 2020, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1027 "add inital new library for processing example, lib_ap_examples.py", 1028 NULL 1029 } , 1030 1031 { 5, Feb, 2020, RCR, "option_list.py", MINOR, TYPE_NEW_OPT, 1032 "list all global options via 'PROG.py -optlist_show_global_opts'", 1033 "Also, add -optlist_show_argv_array to display afni_proc.py options\n" 1034 "in python dictionary format.\n" 1035 "This could be done with any OptionList-based python program." 1036 } , 1037 1038 { 4, Feb, 2020, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 1039 "add help for a few esoteric options", 1040 NULL 1041 } , 1042 1043 { 3, Feb, 2020, RCR, "Dimon", MICRO, TYPE_ENHANCE, 1044 "show CSA data on high debug", 1045 NULL 1046 } , 1047 1048 { 3, Feb, 2020, RCR, "dicom_hdr", MICRO, TYPE_NEW_OPT, 1049 "add -siemens_csa_data", 1050 "Same as 3 -slice_times_verb opts." 1051 } , 1052 1053 { 3, Feb, 2020, RCR, "@SUMA_Make_Spec_FS", MINOR, TYPE_NEW_OPT, 1054 "add -extra_annot_labels", 1055 NULL 1056 } , 1057 1058 { 27, Jan, 2020, RCR, "@SUMA_Make_Spec_FS", MINOR, TYPE_ENHANCE, 1059 "gzip SUMA/*.nii, except for SurfVol", 1060 NULL 1061 } , 1062 1063 { 27, Jan, 2020, RCR, "@diff.tree", MINOR, TYPE_NEW_OPT, 1064 "add -show_list_comp, to do pairwise comparison of file names", 1065 NULL 1066 } , 1067 1068 { 27, Jan, 2020, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 1069 "add basis=BASIS parameter when defining timing class", 1070 "Done for geenaianni on MB." 1071 } , 1072 1073 { 23, Jan, 2020, RCR, "realtime_receiver.py", MINOR, TYPE_ENHANCE, 1074 "add handling of magic version 4 (ROIs and mask==1 data)", 1075 "Done for J Gonzalez-Castillo." 1076 } , 1077 1078 { 22, Jan, 2020, RCR, "plug_realtime", MAJOR, TYPE_GENERAL, 1079 "add ROIs and data mask method", 1080 "Added corresponding demo: AFNI_data6/realtime.demos/demo_3_ROIs_n_data\n" 1081 } , 1082 1083 { 22, Jan, 2020, RCR, "realtime_receiver.py", MINOR, TYPE_ENHANCE, 1084 "add handling of magic version 3 (all data light)", 1085 NULL 1086 } , 1087 1088 { 15, Jan, 2020, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 1089 "corr_* dsets are now correlations with ROI averages", 1090 "They were previously average correlations with each ROI voxel. The new\n" 1091 "maps look similar, but are probably more natural and have nicer scales.\n" 1092 "Requested by P Taylor." 1093 } , 1094 1095 { 13, Jan, 2020, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1096 "add some make lists ; see 'make list_lists'", 1097 NULL 1098 } , 1099 1100 { 2, Jan, 2020, RCR, "plug_realtime", MICRO, TYPE_GENERAL, 1101 "updates corresponding with Javier's new All_Data_light method", 1102 NULL 1103 } , 1104 1105 { 31, Dec, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 1106 "Do not require out_limit. Currently will still show in driver.", 1107 "Done for P Taylor." 1108 } , 1109 1110 { 26, Dec, 2019, RCR, "timing_tool.py", MICRO, TYPE_NEW_OPT, 1111 "add -timing_to_1D_mods and -show_events", 1112 "Done for A Gorka." 1113 } , 1114 1115 { 20, Dec, 2019, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 1116 "add more help details for advanced usage", 1117 NULL 1118 } , 1119 1120 { 17, Dec, 2019, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 1121 "allow labels as column selectors when reading xmat.1D files", 1122 "Done for G Chen." 1123 } , 1124 1125 { 10, Dec, 2019, RCR, "uber_proc.py", MINOR, TYPE_MODIFY, 1126 "separate into main/lib/gui, so one can run -help w/out PyQt4", 1127 NULL 1128 } , 1129 1130 { 9, Dec, 2019, RCR, "3dTagalign", MINOR, TYPE_NEW_OPT, 1131 "add -tagset", 1132 "Coded by T Holroyd." 1133 } , 1134 1135 { 29, Nov, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1136 "add -volreg_opts_ewarp, to pass additional volreg EPI warp options", 1137 "Added for L Fernandino." 1138 } , 1139 1140 { 27, Nov, 2019, RCR, "ROIgrow", MICRO, TYPE_BUG_FIX, 1141 "if PER_NODE, also process label == 0", 1142 "Thanks to K Dembny for noting the problem." 1143 } , 1144 1145 { 21, Nov, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1146 "update babble about FreeSurfer in help", 1147 NULL 1148 } , 1149 1150 { 21, Nov, 2019, RCR, "@auto_tlrc", MINOR, TYPE_BUG_FIX, 1151 "add 'endif' for if( $warpdrive_method == '3dWarpDrive'", 1152 "Thanks to T Holroyd for reporting and fixing this." 1153 } , 1154 1155 { 21, Nov, 2019, RCR, "3dRank", MINOR, TYPE_BUG_FIX, 1156 "fix storage_mode handling (re-allow niml.dset output)", 1157 "Thanks to dmoracze on the Message Board for noting the problem." 1158 } , 1159 1160 { 19, Nov, 2019, RCR, "tedana.py", MICRO, TYPE_BUG_FIX, 1161 "add arr.flags.writeable fallback in volumeutils.py:array_from_file()", 1162 "Done for L Sepeta, for CentoOS 6." 1163 } , 1164 1165 { 19, Nov, 2019, RCR, "@SUMA_Make_Spec_FS", MINOR, TYPE_NEW_OPT, 1166 "add -fs_setup, to optionally source $FREESURFER_HOME/SetUpFreeSurfer.csh", 1167 NULL 1168 } , 1169 1170 { 13, Nov, 2019, RCR, "afni_system_check.py", MICRO, TYPE_MODIFY, 1171 "omit any final PyQt4 warnings unless asked for", 1172 "Done to appease the mighty P Taylor." 1173 } , 1174 1175 { 1, Nov, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1176 "process out.mask_at_corr.txt, the anat/template Dice coefficient", 1177 "Requested by P Hamilton." 1178 } , 1179 1180 { 1, Nov, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1181 "create out.mask_at_corr.txt, the anat/template Dice coefficient", 1182 "Requested by P Hamilton." 1183 } , 1184 1185 { 28, Oct, 2019, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 1186 "fix THD_write_niml to apply directory to output file", 1187 "Thanks to pmlauro on Message Board, for pointing out the problem." 1188 } , 1189 1190 { 25, Oct, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1191 "allow selectors on -dset* options (cannot mix with removal options)", 1192 "Requested by E Finn." 1193 } , 1194 1195 { 24, Oct, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1196 "add combine methods m_tedana, m_tedana_OC", 1197 "Can run tedana from MEICA group:\n" 1198 " https://github.com/ME-ICA/tedana\n" 1199 " https://tedana.readthedocs.io" 1200 } , 1201 1202 { 23, Oct, 2019, RCR, "3dZeropad", MICRO, TYPE_NEW_OPT, 1203 "add -pad2evens: add needed planes to make each dimension even", 1204 NULL 1205 } , 1206 1207 { 21, Oct, 2019, RCR, "afni", MICRO, TYPE_NEW_OPT, 1208 "add -get_running_env, to show env including locally set vars", 1209 NULL 1210 } , 1211 1212 { 17, Oct, 2019, RCR, "3dANOVA", MICRO, TYPE_ENHANCE, 1213 "improve descriptions of some option errors to the user", 1214 NULL 1215 } , 1216 1217 { 17, Oct, 2019, RCR, "3dTcorr1D", MICRO, TYPE_BUG_FIX, 1218 "strcasestr fix subsumed by adding _GNU_SOURCE to make", 1219 "Undo removal of strcasestr." 1220 } , 1221 1222 { 17, Oct, 2019, RCR, "Makefile", MICRO, TYPE_BUG_FIX, 1223 "for strcasestr, we need to define _GNU_SOURCE in Makefile.*", 1224 NULL 1225 } , 1226 1227 { 16, Oct, 2019, RCR, "@auto_tlrc", MINOR, TYPE_ENHANCE, 1228 "re-insert updates from 2019.05.29, plus updates for -init_xform", 1229 NULL 1230 } , 1231 1232 { 16, Oct, 2019, RCR, "3dFFT", MICRO, TYPE_ENHANCE, 1233 "process entire time series, rather than just the first volume", 1234 "Done for A Khojandi." 1235 } , 1236 1237 { 16, Oct, 2019, RCR, "TwotoComplex", MICRO, TYPE_ENHANCE, 1238 "process entire time series, rather than just first volume(s)", 1239 "Done to further the quest of A Khojandi for world domination." 1240 } , 1241 1242 { 15, Oct, 2019, RCR, "3dinfo", MINOR, TYPE_NEW_OPT, 1243 "add -subbrick_info, to write only 'At sub-brick #N' info to stdout", 1244 NULL 1245 } , 1246 1247 { 11, Oct, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1248 "checked and merged another 17 commit PR from pn2200", 1249 "This is mostly to resolve missing prototypes." 1250 } , 1251 1252 { 10, Oct, 2019, RCR, "3dinfo", MINOR, TYPE_NEW_OPT, 1253 "add -niml_hdr, to write full NIML header(s) to stdout", 1254 NULL 1255 } , 1256 1257 { 10, Oct, 2019, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 1258 "search for niml.dset errts datasets", 1259 NULL 1260 } , 1261 1262 { 10, Oct, 2019, RCR, "afni_base.py", MICRO, TYPE_BUG_FIX, 1263 "in NIML case, exist should check ppv file directly", 1264 NULL 1265 } , 1266 1267 { 9, Oct, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1268 "checked and merged 30 commit PR from pn2200", 1269 "This is mostly to resolve compiler warnings." 1270 } , 1271 1272 { 7, Oct, 2019, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 1273 "probably the last set of test updates for now", 1274 NULL 1275 } , 1276 1277 { 4, Oct, 2019, RCR, "3dNLfim", MICRO, TYPE_BUG_FIX, 1278 "allow for longer input and output file names", 1279 "Names were malloc'd with MAX_NAME_LENGTH; use nifti_strdup, instead.\n" 1280 "Thanks to S Wardle for bringing this to light." 1281 } , 1282 1283 { 30, Sep, 2019, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 1284 "added test scripts under commands, along with cmake versions for build", 1285 NULL 1286 } , 1287 1288 { 26, Sep, 2019, RCR, "NIFTI", MICRO, TYPE_MODIFY, 1289 "nifti_read_ascii_image no longer closes fp or free's fname", 1290 NULL 1291 } , 1292 1293 { 23, Sep, 2019, RCR, "@update.afni.binaries", MICRO, TYPE_BUG_FIX, 1294 "missed endif", 1295 "Thanks to A Winkler for noting the problem." 1296 } , 1297 1298 { 18, Sep, 2019, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 1299 "if -html_review_style pythonic, check for matplotlib", 1300 NULL 1301 } , 1302 1303 { 16, Sep, 2019, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 1304 "check on /usr/local/bin/python* files, as is done with /sw/bin", 1305 NULL 1306 } , 1307 1308 { 13, Sep, 2019, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 1309 "report XQuartz version", 1310 "As suggested by P Taylor." 1311 } , 1312 1313 { 12, Sep, 2019, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 1314 "add file tracking and -show_tracked_files option", 1315 "In preparation for shifting evil for P Taylor and D Glen." 1316 } , 1317 1318 { 9, Sep, 2019, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 1319 "add control for 3dDespike -NEW25", 1320 "Requested by aparekh on the Message Board." 1321 } , 1322 1323 { 5, Sep, 2019, RCR, "SurfMeasures", MICRO, TYPE_MODIFY, 1324 "retab and fix indentations", 1325 NULL 1326 } , 1327 1328 { 4, Sep, 2019, RCR, "@SUMA_Make_Spec_FS", MICRO, TYPE_ENHANCE, 1329 "check for valid 'mris_convert --help' output", 1330 NULL 1331 } , 1332 1333 { 26, Aug, 2019, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 1334 "report 'R RHOME'", 1335 NULL 1336 } , 1337 1338 { 27, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1339 "linux_fedora_28_shared: make libf2c.so as a shared object", 1340 "2.4 GB binaries -> (libmri.so) 600 MB -> (libSUMA.so) 202 MB\n" 1341 " -> (libf2c.so) 190 MB" 1342 } , 1343 1344 { 26, Aug, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1345 "linux_fedora_28_shared: make libSUMA.so as a shared object", 1346 "2.4 GB binaries -> (libmri.so) 600 MB -> (libSUMA.so) 200 MB" 1347 } , 1348 1349 { 26, Aug, 2019, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 1350 "check for dyn.load error via 3dMVM", 1351 NULL 1352 } , 1353 1354 { 23, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1355 "updates corresponding to Travis CI OS change: Ubuntu 14->16", 1356 "Set .travis.yml to use OS_notes.linux_ubuntu_16_64 for system udpate,\n" 1357 "and update the notes to include fix of GLwDrawA.h.\n" 1358 "Also, seem to need to enable mysql." 1359 } , 1360 1361 { 22, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1362 "THD_write_atr(): make the Kris K condition do more aggressive napping", 1363 "More aggressive napping?!?\n" 1364 "Sleep 6 times for 2^(n+1) seconds, up to ~1 min, for a total of ~2 min." 1365 } , 1366 1367 { 22, Aug, 2019, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 1368 "(w/dglen) thd_gifti: remove INDEX_LIST DA from from list", 1369 "When converting a GIFTI dataset to NIML, any index list should be\n" 1370 "separated early, so as not to affect the SPARSE_DATA NIML element.\n" 1371 "Thanks to T Holroyd for noting the problem." 1372 } , 1373 1374 { 19, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1375 "Makefile.INCLUDE: add libmri target, for build system", 1376 "Let the make system decide whether it should be a shared lib.\n" 1377 "Also, make install_plugins just plug*.so model*.so and have\n" 1378 "itall target depend on install_lib." 1379 } , 1380 1381 { 19, Aug, 2019, RCR, "3dDeconvolve_f", MINOR, TYPE_BUG_FIX, 1382 "matrix_f.[ch]: dupe matrix_augment_01_columns from matrix.[ch]", 1383 "When choosing between more local functions and those included in a\n" 1384 "linked library, some systems seem to go all-or-nothing for one file\n" 1385 "at a time. So for 3dDeconvolve_f, matrix_f.c needs everything that\n" 1386 "might come from matrix.c. Otherwise we should have matrix_f.h rename\n" 1387 "all of those functions, to avoid relying on compiler choices." 1388 } , 1389 1390 { 16, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1391 "(w/dglen) in THD_write_atr(), give file opening multiple opertunities", 1392 "Done for K Knutson." 1393 } , 1394 1395 { 15, Aug, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1396 "build R_io.so with usable link to libmri.so", 1397 "Modify Makefile.linux_fedora_28_shared and Makefile.INCLUDE to control\n" 1398 "creation of Makevars via R_IO_MODIFY_LINUX." 1399 } , 1400 1401 { 15, Aug, 2019, RCR, "afni-general", MINOR, TYPE_GENERAL, 1402 "add other_builds/OS_notes.linux_fedora_30.txt", 1403 "Works with Makefile.linux_fedora_28_shared." 1404 } , 1405 1406 { 13, Aug, 2019, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 1407 "fix -VXXXX= for real operating systems", 1408 NULL 1409 } , 1410 1411 { 13, Aug, 2019, RCR, "RetroTS.py", MICRO, TYPE_GENERAL, 1412 "RVT_from_PeakFinder.py: remove unused plot()", 1413 NULL 1414 } , 1415 1416 { 12, Aug, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1417 "python3 compatibility", 1418 "Including: make_stim_times.py, python_module_test.py, lib_matplot.py,\n" 1419 " slow_surf_clustsim.py, lib_surf_clustsim.py, make_pq_script.py." 1420 } , 1421 1422 { 8, Aug, 2019, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 1423 "be more merciful in the case of timing overlap", 1424 " - ISI stats: allow and adjust for stim overlap\n" 1425 " - dur stats: show file/condition with stats\n" 1426 " - match output between python2 and python3" 1427 } , 1428 1429 { 7, Aug, 2019, RCR, "rPkgsInstall", MINOR, TYPE_ENHANCE, 1430 "more programs that need R_LD_LIBRARY_PATH", 1431 "Full list: 1dRplot, 3dICC, 3dISC, 3dLME, 3dMEMA, 3dMEPFM, 3dMVM, 3dPFM,\n" 1432 " 3dRprogDemo, 3dSignatures, ExamineXmat, MBA, RBA, rPkgsInstall." 1433 } , 1434 1435 { 5, Aug, 2019, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 1436 "check for matplotlib.pyplot", 1437 NULL 1438 } , 1439 1440 { 5, Aug, 2019, RCR, "3dMVM", MINOR, TYPE_MODIFY, 1441 "set R_LD_LIBRARY_PATH for all 3d* R-calling programs using $afpath on osx", 1442 "For macs: to allow R_io.so to load shared libraries needed by libmri,\n" 1443 " set the search path to include the abin, flat_namespace and\n" 1444 " R lib dir.\n" 1445 "This might apply to linux with libmri.so, as well.\n" 1446 "Thanks to N Adleman, C Caballero and E Silson." 1447 } , 1448 1449 { 30, Jul, 2019, RCR, "gen_group_command.py", MICRO, TYPE_ENHANCE, 1450 "format help output for sphinx conversion", 1451 NULL 1452 } , 1453 1454 { 29, Jul, 2019, RCR, "timing_tool.py", MICRO, TYPE_ENHANCE, 1455 "format help output for sphinx conversion", 1456 NULL 1457 } , 1458 1459 { 26, Jul, 2019, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 1460 "add -make_backup and -echo", 1461 "Suggested by J Rajendra." 1462 } , 1463 1464 { 25, Jul, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1465 "add -volreg_warp_master, for controlling the output grid", 1466 "Added for Y Miyawaki." 1467 } , 1468 1469 { 24, Jul, 2019, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 1470 "add -show_tsv_label_details option", 1471 NULL 1472 } , 1473 1474 { 23, Jul, 2019, RCR, "timing_tool.py", MICRO, TYPE_ENHANCE, 1475 "add -tsv_labels option help and examples", 1476 NULL 1477 } , 1478 1479 { 19, Jul, 2019, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 1480 "if template is multi-volume, get vol [0] for group_mask", 1481 "Thanks to S Tumati for noting the problem." 1482 } , 1483 1484 { 19, Jul, 2019, RCR, "nifti_tool", MINOR, TYPE_ENHANCE, 1485 "add use of HDR/NIM_SLICE_TIMING_FIELDS for -field option", 1486 "This allows -{disp,diff}_{hdr,nim} an easy specification of\n" 1487 "fields related to slice timing." 1488 } , 1489 1490 { 18, Jul, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1491 "look for multi-echo data in find_tcat", 1492 NULL 1493 } , 1494 1495 { 17, Jul, 2019, RCR, "NIFTI", MINOR, TYPE_BUG_FIX, 1496 "another fix for 32-64 bit NIFTI update for older xorg7 systems", 1497 "In thd_niftiread.c, cast nim->nz as int for EDIT_dset_items().\n" 1498 "Newer C libraries seem to handle the possibility of 8 bits better,\n" 1499 "but we are reading as 4. Thanks again to R Birn." 1500 } , 1501 1502 { 17, Jul, 2019, RCR, "NIFTI", MICRO, TYPE_BUG_FIX, 1503 "fix inappropriate 'dimensions altered' warning on xorg7", 1504 "Warning: dimensions altered since AFNI extension was added\n" 1505 "Use PRId64 for 64-bit int printing, works on old systems, too.\n" 1506 "Thanks to R Birn for noting the problem." 1507 } , 1508 1509 { 5, Jul, 2019, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 1510 "(useless) switch to 3dTcorr1D for dot product", 1511 "Drops 2 commands down to 1 for computing corr_* volumes." 1512 } , 1513 1514 { 3, Jul, 2019, RCR, "3dvolreg", MICRO, TYPE_BUG_FIX, 1515 "make 'second -zpad option' warning appropriate again", 1516 NULL 1517 } , 1518 1519 { 3, Jul, 2019, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 1520 "let X.stim.xmat.1D be empty for non-task case", 1521 NULL 1522 } , 1523 1524 { 3, Jul, 2019, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 1525 "if no stim, create sum_baseline.1D, rather than sum_ideal.1D", 1526 NULL 1527 } , 1528 1529 { 3, Jul, 2019, RCR, "1d_tool.py", MICRO, TYPE_BUG_FIX, 1530 "allow writing of empty stim files ($status 0)", 1531 NULL 1532 } , 1533 1534 { 2, Jul, 2019, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 1535 "create X.stim.xmat.1D via 1d_tool.py -write_xstim, to keep labels", 1536 NULL 1537 } , 1538 1539 { 1, Jul, 2019, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 1540 "add complex Example 13; add use of @SSwarper outputs in Example 11", 1541 NULL 1542 } , 1543 1544 { 28, Jun, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1545 "add vr_base_dset uvar", 1546 NULL 1547 } , 1548 1549 { 27, Jun, 2019, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 1550 "add -write_with_header and -write_xstim", 1551 NULL 1552 } , 1553 1554 { 25, Jun, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1555 "get TSNR on surface", 1556 NULL 1557 } , 1558 1559 { 19, Jun, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1560 "add surf_vol uvar", 1561 NULL 1562 } , 1563 1564 { 19, Jun, 2019, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 1565 "actually fail for some inappropriate blur options with surface analysis", 1566 NULL 1567 } , 1568 1569 { 18, Jun, 2019, RCR, "3dGrayplot", MICRO, TYPE_ENHANCE, 1570 "allow grayplot of surface data if not -peelorder", 1571 NULL 1572 } , 1573 1574 { 18, Jun, 2019, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 1575 "no mask if TSNR on surface", 1576 "Thanks to K Dembny for noting the problem." 1577 } , 1578 1579 { 14, Jun, 2019, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 1580 "add -hostname and -distdir", 1581 "This is to allow places to mirror some of the AFNI site." 1582 } , 1583 1584 { 14, Jun, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1585 "add Makefile.linux_fedora_28_shared, to distribute a shared lib package", 1586 "This uses libmri.so, though other libraries should be added (SUMA).\n" 1587 "R programs do not yet work, as linking for R_io.so needs to be fixed." 1588 } , 1589 1590 { 13, Jun, 2019, RCR, "afni_base.py", MICRO, TYPE_ENHANCE, 1591 "allow for enclosed variables in afni_name, e.g. '${subj}'", 1592 NULL 1593 } , 1594 1595 { 12, Jun, 2019, RCR, "Makefile.INCLUDE", MINOR, TYPE_MODIFY, 1596 "better prep for shared build, and fix shared build of suma_gts_progs", 1597 "Move mri_render.o out of libmri (corresponds with plug_render.so)." 1598 "Still need to fix mpeg_encode." 1599 } , 1600 1601 { 10, Jun, 2019, RCR, "afni-general", MICRO, TYPE_MODIFY, 1602 "apply FreeBSD patches from J Bacon", 1603 " - afni_xml.h: include inttypes.h\n" 1604 " - prf_common_circular.c: use malloc_stats_print()\n" 1605 " - Makefile.ptaylor.INCLUDE: add -fopenmp for building 3dDWUncert" 1606 } , 1607 1608 { 6, Jun, 2019, RCR, "@auto_tlrc", MICRO, TYPE_MODIFY, 1609 "back off recent updates - need to resolve -init_xform", 1610 "Thanks to H Keren for letting us know of the problem." 1611 } , 1612 1613 { 4, Jun, 2019, RCR, "3dinfo", MINOR, TYPE_NEW_OPT, 1614 "add -dset_extension, -storage_mode", 1615 NULL 1616 } , 1617 1618 { 4, Jun, 2019, RCR, "plug_tag", MINOR, TYPE_BUG_FIX, 1619 "use calloc to init last 4 bytes of tag string in thd_dsetatr.c", 1620 "This was leaving garbage in HEAD file.\n" 1621 "Thanks to A Nugent for noting the problem." 1622 } , 1623 1624 { 3, Jun, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1625 "allow ricor processing in case of multi-echo data", 1626 "Done for K Dembny." 1627 } , 1628 1629 { 30, May, 2019, RCR, "@radial_correlate", MINOR, TYPE_MODIFY, 1630 "apply full Gaussian for blur, rather than truncated", 1631 "Truncated is okay, but has cubical extents, rather than spherical." 1632 } , 1633 1634 { 23, May, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1635 "add options -regress_anaticor_full_gaussian, -regress_anaticor_term_frac", 1636 "Also, save fanaticor_mask_coverage dataset." 1637 } , 1638 1639 { 22, May, 2019, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 1640 "blurs are now truncated Gaussians by default, making them flat", 1641 NULL 1642 } , 1643 1644 { 22, May, 2019, RCR, "Makefile.INCLUDE", MICRO, TYPE_GENERAL, 1645 "start with 'MAKE ?= make', and use MAKE exclusively", 1646 "Thanks to J Bacon for the suggestion." 1647 } , 1648 1649 { 20, May, 2019, RCR, "plug_vol2surf", MINOR, TYPE_BUG_FIX, 1650 "modify pane_scale to match updates for AFNI_PBAR_FULLRANGE", 1651 NULL 1652 } , 1653 1654 { 16, May, 2019, RCR, "gen_ss_review_scripts", MINOR, TYPE_ENHANCE, 1655 "add uvars flip_check_dset and flip_guess", 1656 "Add 'flip guess' to review_basic output." 1657 } , 1658 1659 { 16, May, 2019, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 1660 "add read_text_dictionary, read_text_dict_list, convert_table2dict", 1661 "Also, allow table2dict in write_data_as_json. This allows for easy I/O\n" 1662 "of tables, and the ability to convert them to json form." 1663 } , 1664 1665 { 15, May, 2019, RCR, "gen_ss_review_scripts", MINOR, TYPE_ENHANCE, 1666 "add uvar have_radcor_dirs", 1667 NULL 1668 } , 1669 1670 { 15, May, 2019, RCR, "@radial_correlate", MINOR, TYPE_ENHANCE, 1671 "modify output file names to handle special cases of all_runs and errts", 1672 NULL 1673 } , 1674 1675 { 14, May, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1676 "add options -radial_correlate_blocks and -radial_correlate_opts", 1677 "Run @raidal_correlate at the end of each specified block, creating one\n" 1678 "correlation volume per run. Each voxel gets the correlation of its time\n" 1679 "series with a local (slighly Gaussian weighted) average." 1680 } , 1681 1682 { 13, May, 2019, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 1683 "fail if using MIN_OUTLIER, but not enough time points", 1684 "Thanks to H Mandelkow for noting this." 1685 } , 1686 1687 { 10, May, 2019, RCR, "NIFTI", MICRO, TYPE_ENHANCE, 1688 "add NIFTI_ECODE_QUANTIPHYSE", 1689 NULL 1690 } , 1691 1692 { 9, May, 2019, RCR, "3dTcorrelate", MICRO, TYPE_ENHANCE, 1693 "include old history of xset", 1694 NULL 1695 } , 1696 1697 { 9, May, 2019, RCR, "@radial_correlate", MINOR, TYPE_NEW_OPT, 1698 "replace 3dLocalstat with 3dmerge for locally ~averaged time series", 1699 "One can choose between the methods, but 3dmerge is much faster.\n" 1700 "Included options are -use_3dmerge, -corr_mask and -merge_nrad,\n" 1701 "as well as -do_clean and -verb." 1702 } , 1703 1704 { 8, May, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1705 "allow AFNI_BLUR_FIRFAC to get near zero", 1706 "This can be abused for a 'fast ANATICOR', for example.\n" 1707 "Since sigma = 0.4246609 * fwhm, consider using: \n" 1708 " sfac = 1/(2*.0.4246609) = 1.17741\n" 1709 "That number of sigmas should match the half width at half max,\n" 1710 "which should terminate the blur just after a half height.\n" 1711 "\n" 1712 "Or use 2*FWHM and sfac = 1.17741/2 = 0.588705 to make it more flat,\n" 1713 "with a min contribution of ~0.84, rather than 0.5, yet limiting\n" 1714 "the output to the same HWHM radius (e.g. FWHM=80mm with sfac=0.589\n" 1715 "results in a fairly flat blur out to a radius of ~20 mm)." 1716 } , 1717 1718 { 8, May, 2019, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 1719 "add -module_dir", 1720 NULL 1721 } , 1722 1723 { 7, May, 2019, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 1724 "add -timing_to_1D_warn_ok to make some conversion issues non-fatal", 1725 "Done for J Wiggins and M Liuzzi." 1726 } , 1727 1728 { 7, May, 2019, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 1729 "add deg2chordlen() to return distance traveled due to a rotation", 1730 NULL 1731 } , 1732 1733 { 25, Apr, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1734 "-regress_bandpass now takes any positive number of frequencies pairs", 1735 "Done to appease the mighty P Taylor." 1736 } , 1737 1738 { 23, Apr, 2019, RCR, "3dAllineate", MICRO, TYPE_ENHANCE, 1739 "Allow '^' to denote a power in -autoweight, in addition to '**'\n", 1740 "This is to avoid protecting the string in quotes, making it easy\n" 1741 "to pass from afni_proc.py to align_epi_anat.py to 3dAllineate." 1742 } , 1743 1744 { 22, Apr, 2019, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 1745 "add -tsv_labels", 1746 "This can be used to specify column labels to be used for\n" 1747 "onset time, duration, trial type, and optional modulators." 1748 } , 1749 1750 { 16, Apr, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_BUG_FIX, 1751 "verify av_space == +tlrc before setting template", 1752 "Thanks to P Molfese and P Taylor for noting the problem." 1753 } , 1754 1755 { 16, Apr, 2019, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 1756 "if do_apearch, update .bashrc to source all_progs.COMP.bash", 1757 "Done to appease the mighty P Taylor." 1758 } , 1759 1760 { 11, Apr, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1761 "add -combine_tedort_reject_midk", 1762 "It might be a good idea to set this to 'no', so less gets rejected." 1763 } , 1764 1765 { 11, Apr, 2019, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 1766 "add functions gaussian_at_fwhm, gaussian_at_hwhm_frac", 1767 NULL 1768 } , 1769 1770 { 8, Apr, 2019, RCR, "@extract_meica_ortvec", MINOR, TYPE_NEW_OPT, 1771 "add options -reject_midk and -reject_ignored", 1772 "It seems likely that '-reject_midk 0' should be the default." 1773 } , 1774 1775 { 20, Mar, 2019, RCR, "dcm2niix_afni", MINOR, TYPE_BUG_FIX, 1776 "sync crorden/dcm2niix_console with repo, version v1.0.20181125", 1777 "This is possibly to correct a bug with -m and partial brain coverage." 1778 } , 1779 1780 { 15, Mar, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1781 "include tr field in uvars, and report it as TR in basic", 1782 NULL 1783 } , 1784 1785 { 15, Mar, 2019, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 1786 "in any dotfile update: note that it was done by @uab", 1787 NULL 1788 } , 1789 1790 { 14, Mar, 2019, RCR, "GIFTI", MINOR, TYPE_ENHANCE, 1791 "add gifti/regress_tests tree", 1792 "This was also added to https://github.com/NIFTI-Imaging/gifti_clib repo." 1793 } , 1794 1795 { 13, Mar, 2019, RCR, "tedana.py", MICRO, TYPE_MODIFY, 1796 "default to system nibabel over local", 1797 "Need to ponder what to do with local nibabel. This will move us towards\n" 1798 "omitting it, though we plan to move away from AFNI's tedana.py, too." 1799 } , 1800 1801 { 7, Mar, 2019, RCR, "gen_ss_review_table.py", MAJOR, TYPE_NEW_OPT, 1802 "add -report_outliers and support options", 1803 "Add -report_outliers_{fill,header}_style, -write_outlier, and\n" 1804 " -outlier_sep for controlling the table presentation.\n" 1805 "Will use -write_table instead of -tablefile going forward." 1806 } , 1807 1808 { 7, Mar, 2019, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 1809 "tee output from @ss_review_html to a text file", 1810 "Done for P Taylor." 1811 } , 1812 1813 { 6, Mar, 2019, RCR, "Dimon", MINOR, TYPE_ENHANCE, 1814 "if VR mismatch warning, specify whether AFNI uses the field", 1815 "Done for B Benson." 1816 } , 1817 1818 { 5, Mar, 2019, RCR, "gen_group_command.py", MINOR, TYPE_ENHANCE, 1819 "show subject counts; change line len and ddirs; no require on restricted", 1820 NULL 1821 } , 1822 1823 { 28, Feb, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_BUG_FIX, 1824 "mask dset must include extension", 1825 NULL 1826 } , 1827 1828 { 26, Feb, 2019, RCR, "gen_group_command.py", MINOR, TYPE_NEW_OPT, 1829 "add -dset_sid_list, -hpad, -tpad", 1830 "Add -dset_sid_list to specify subject IDs explicitly.\n" 1831 "Also, add -hpad/-tpad; less indentation for 3dttest++." 1832 } , 1833 1834 { 25, Feb, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1835 "try to get mask_dset from TSNR output", 1836 NULL 1837 } , 1838 1839 { 25, Feb, 2019, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 1840 "add modulators to -multi_timing_to_event_list output", 1841 "Done for D Jangraw." 1842 } , 1843 1844 { 22, Feb, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1845 "add -tlrc_NL_force_view, to handle sform_code=2 in auto_warp.py result", 1846 "Done for I Berteletti." 1847 } , 1848 1849 { 22, Feb, 2019, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 1850 "handle shells with paths in get_current/login_shell()", 1851 NULL 1852 } , 1853 1854 { 8, Feb, 2019, RCR, "3dWarp", MICRO, TYPE_NEW_OPT, 1855 "add -wsinc5", 1856 NULL 1857 } , 1858 1859 { 7, Feb, 2019, RCR, "demoExpt.py", MINOR, TYPE_NEW_PROG, 1860 "will now actually distribute Vinai's demoExpt.py and afniInterfaceRT", 1861 NULL 1862 } , 1863 1864 { 5, Feb, 2019, RCR, "Dimon", MINOR, TYPE_MODIFY, 1865 "-infile_list now implies -no_wait", 1866 NULL 1867 } , 1868 1869 { 5, Feb, 2019, RCR, "3dinfo", MINOR, TYPE_BUG_FIX, 1870 "allow -extent to vary across datasets", 1871 NULL 1872 } , 1873 1874 { 5, Feb, 2019, RCR, "demoExpt.py", MICRO, TYPE_GENERAL, 1875 "add roopchansinghv to afni_src.tgz target", 1876 "This is a realtime neurofeedback framework, built on top of afni and\n" 1877 "realtime_receiver.py, using PsychoPy for feedback and presentation.\n" 1878 "Also, set demoExpt.py mode as 755." 1879 } , 1880 1881 { 4, Feb, 2019, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 1882 "use abs in dims check for -mask_import", 1883 NULL 1884 } , 1885 1886 { 30, Jan, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1887 "add -volreg_post_vr_allin and -volreg_pvra_base_index", 1888 "These are to run 3dvolreg (or 3dAllineate) to a base within\n" 1889 "each run, before concatenating a transformation from each\n" 1890 "per-run base to the global EPI registration base." 1891 } , 1892 1893 { 28, Jan, 2019, RCR, "3dttest++", MICRO, TYPE_ENHANCE, 1894 "output volume counts for -set options", 1895 NULL 1896 } , 1897 1898 { 28, Jan, 2019, RCR, "afni-general", MINOR, TYPE_ENHANCE, 1899 "updates to make target, prog_list", 1900 " - grep out CMakeLists.txt\n" 1901 " - add some ptaylor python scripts\n" 1902 " - define and add DISCO_SCRIPTS" 1903 } , 1904 1905 { 28, Jan, 2019, RCR, "afni-general", MINOR, TYPE_NEW_OPT, 1906 "add -help to @djunct_*.py", 1907 NULL 1908 } , 1909 1910 { 22, Jan, 2019, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 1911 "add -show_obsoletes[_grep] and -show_system_progs", 1912 "Inspired by Z Saad." 1913 } , 1914 1915 { 22, Jan, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1916 "added -regress_est_blur_detrend", 1917 "We might change the default to no detrending here." 1918 } , 1919 1920 { 18, Jan, 2019, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 1921 "process df_info, and hand off new uvars", 1922 NULL 1923 } , 1924 1925 { 18, Jan, 2019, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 1926 "run 1d_tool.py -show_df_info, unless -regress_show_df_info no", 1927 NULL 1928 } , 1929 1930 { 17, Jan, 2019, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 1931 "add option -show_df_info, to partition degrees of freedom in X-matrix", 1932 NULL 1933 } , 1934 1935 { 16, Jan, 2019, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 1936 "-regress_mot_as_ort now defaults to yes; use vr_base_external", 1937 "This should not affect results, it is prep for other evil designs." 1938 } , 1939 1940 { 11, Jan, 2019, RCR, "dicom_hinfo", MICRO, TYPE_NEW_OPT, 1941 "add -sepstr option", 1942 "Done for ZXu on message board." 1943 } , 1944 1945 { 8, Jan, 2019, RCR, "afni-general", MICRO, TYPE_ENHANCE, 1946 "add make targets prog_list_bin and _scripts, which generate prog_list.txt", 1947 "This is done to partition binaries vs scripts." 1948 } , 1949 1950 { 8, Jan, 2019, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 1951 "add -volreg_method, and corresponding options", 1952 "This allows one to use 3dAllineate for EPI motion registration.\n" 1953 "Options -volreg_allin_cost and -volreg_allin_auto_stuff (as well as\n" 1954 "the old -volreg_opts_vr) can be used to control -cost and other options." 1955 } , 1956 1957 { 4, Jan, 2019, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 1958 "add regression testing scripts", 1959 NULL 1960 } , 1961 1962 { 4, Jan, 2019, RCR, "nifti_tool", MINOR, TYPE_MODIFY, 1963 "add -mod_hdr2, specific to NIFTI-2 headers", 1964 NULL 1965 } , 1966 1967 { 3, Jan, 2019, RCR, "nifti_tool", MINOR, TYPE_MODIFY, 1968 "have -mod_hdr/-swap_as_nifti fail on valid NIFTI-2 header", 1969 "Re-allow processing of ASCII headers (via NIFTI-2).\n" 1970 "Also, incorporate updates from H Johnson." 1971 } , 1972 1973 { 26, Dec, 2018, RCR, "afni-general", MINOR, TYPE_MODIFY, 1974 "incorporate more updates from the NIFTI_Imaging/nifti_clib repo", 1975 NULL 1976 } , 1977 1978 { 20, Dec, 2018, RCR, "afni-general", MINOR, TYPE_MODIFY, 1979 "incorporate updates from the NIFTI_Imaging/nifti_clib repo", 1980 "And update Makefile.INCLUDE." 1981 } , 1982 1983 { 19, Dec, 2018, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 1984 "show execution syntax in both tcsh and bash", 1985 "Done to appease the mighty P Taylor." 1986 } , 1987 1988 { 14, Dec, 2018, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 1989 "include mask and params in -csim_show_clustsize", 1990 NULL 1991 } , 1992 1993 { 13, Dec, 2018, RCR, "@strip.whitespace", MINOR, TYPE_NEW_PROG, 1994 "stored under scripts_src; guess what it does", 1995 NULL 1996 } , 1997 1998 { 13, Dec, 2018, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 1999 "removed nift1-test from the distribution", 2000 NULL 2001 } , 2002 2003 { 13, Dec, 2018, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2004 "merged NIFTI updates from NIFTI-Imaging/nifti_clib repo", 2005 NULL 2006 } , 2007 2008 { 11, Dec, 2018, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 2009 "use mkdir -p; reconcile write_as_nifti and NIFTI prefix", 2010 "Thanks to C Smith for noting the issue." 2011 } , 2012 2013 { 4, Dec, 2018, RCR, "afni-general", MINOR, TYPE_ENHANCE, 2014 "Makefiles: working towards using libmri.so", 2015 "Pass MRI_SHARED, and apply with SUMA_SHARED_LOPTS in SUMA." 2016 } , 2017 2018 { 3, Dec, 2018, RCR, "test.afni.prog.help", MINOR, TYPE_NEW_PROG, 2019 "test running -help on AFNI programs", 2020 "This is a build tool, not for the distribution." 2021 } , 2022 2023 { 3, Dec, 2018, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 2024 "use LIBMRI_OBJ = libmri.a, for future evil", 2025 NULL 2026 } , 2027 2028 { 27, Nov, 2018, RCR, "apqc_make_tcsh.py", MICRO, TYPE_ENHANCE, 2029 "python3 update for chmod code", 2030 "Thanks to L Dowdle for noting the issue." 2031 } , 2032 2033 { 26, Nov, 2018, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 2034 "add opt -volreg_warp_final_interp", 2035 "This controls final interpolation for all non-NN warps, including\n" 2036 "catenated EPI transforms (affine and non-linear), final EPI,\n" 2037 "and anatomical followers.\n" 2038 "Done for \"the boss\"." 2039 } , 2040 2041 { 21, Nov, 2018, RCR, "3dcopy", MICRO, TYPE_ENHANCE, 2042 "try to append HISTORY for non-AFNI datasets", 2043 NULL 2044 } , 2045 2046 { 19, Nov, 2018, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 2047 "add opt -html_review_style and run apqc_make_html.py", 2048 NULL 2049 } , 2050 2051 { 19, Nov, 2018, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 2052 "run any review scripts before possibly [re-]moving preproc data", 2053 NULL 2054 } , 2055 2056 { 17, Nov, 2018, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2057 "add epiphany and midori as browser candidates (11/21 google-chrome)", 2058 NULL 2059 } , 2060 2061 { 14, Nov, 2018, RCR, "3dDeconvolve", MICRO, TYPE_ENHANCE, 2062 "update 3dREMLfit command to handle surface data", 2063 "Strip off the .niml.dset extension, if found in the bucket name.\n" 2064 "Is it better to re-append it? I am not sure." 2065 } , 2066 2067 { 5, Nov, 2018, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 2068 "enhance insufficient time warnings", 2069 NULL 2070 } , 2071 2072 { 29, Oct, 2018, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2073 "zsh: check for .zshenv", 2074 NULL 2075 } , 2076 2077 { 29, Oct, 2018, RCR, "FSread_annot", MICRO, TYPE_ENHANCE, 2078 "fix crash and more clearly warn if missing FSColorLUT file", 2079 NULL 2080 } , 2081 2082 { 17, Oct, 2018, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 2083 "add uvar xmat_stim", 2084 NULL 2085 } , 2086 2087 { 17, Oct, 2018, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2088 "pass -ss_review_dset to gen_ss_review_scripts.py", 2089 NULL 2090 } , 2091 2092 { 16, Oct, 2018, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2093 "if no AFNI errors, skip homebrew library linking warnings", 2094 NULL 2095 } , 2096 2097 { 16, Oct, 2018, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 2098 "added new uvar fields", 2099 "Move g_ss_uvar_fields to lib_ss_review.py.\n" 2100 "Add uvar fields: nt_applied, nt_orig, ss_review_dset,\n" 2101 " pre_ss_warn_dset, decon_err_dset, tent_warn_dset." 2102 } , 2103 2104 { 16, Oct, 2018, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 2105 "darwin defaults to 10.12; newline before dotfile appends", 2106 NULL 2107 } , 2108 2109 { 11, Oct, 2018, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2110 "check for consistency between python and PyQt4 ", 2111 NULL 2112 } , 2113 2114 { 11, Oct, 2018, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2115 "have gen_ss_review_scripts.py always write out.gen_ss_uvars.json", 2116 "This is to help occupy Paul." 2117 } , 2118 2119 { 9, Oct, 2018, RCR, "make_random_timing.py", MINOR, TYPE_BUG_FIX, 2120 "fix decay rest with non-zero min; block unlimited decay stim dur", 2121 "Thanks to D Plunkett for noting the problem." 2122 } , 2123 2124 { 5, Oct, 2018, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 2125 "directly go after expected column headers in TSV files", 2126 NULL 2127 } , 2128 2129 { 4, Oct, 2018, RCR, "@update.afni.binaries", MICRO, TYPE_BUG_FIX, 2130 "wget/curl may remove execute permision, so re-add it", 2131 NULL 2132 } , 2133 2134 { 1, Oct, 2018, RCR, "gifti_tool", MICRO, TYPE_MODIFY, 2135 "link to nifti2_io.o, rather than nifti1_io.o", 2136 "Also, install nifti2_io.h rather than nifti2_io.h with other headers." 2137 } , 2138 2139 { 1, Oct, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2140 "mri_dicom_hdr.c: init vars in DICOM reading functions", 2141 NULL 2142 } , 2143 2144 { 27, Sep, 2018, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 2145 "added macos_10.12 examples to help", 2146 NULL 2147 } , 2148 2149 { 27, Sep, 2018, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 2150 "handle FSL timing files with fewer than 3 columns", 2151 "For T Radman." 2152 } , 2153 2154 { 25, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2155 "have programs return 0 on -help", 2156 "Adding: fat_lat_csv.py, fat_proc_grad_plot." 2157 } , 2158 2159 { 25, Sep, 2018, RCR, "prog_list.txt", MICRO, TYPE_MODIFY, 2160 "update prog_list.txt from 'make prog_list'; we might remove this file", 2161 NULL 2162 } , 2163 2164 { 25, Sep, 2018, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 2165 "fix first timediff in -multi_timing_to_event_list", 2166 NULL 2167 } , 2168 2169 { 24, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2170 "have programs return 0 on terminal options, like -help", 2171 "Adding: mpeg_encode, cjpeg, djpeg, fat_roi_row.py, fat_mvm_scripter.py,\n" 2172 " fat_mat_sel.py, fat_mvm_prep.py, fat_mvm_review.py." 2173 } , 2174 2175 { 21, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2176 "separate testGL build target from SUMA_PROGS", 2177 "Again, for accuracy of 'make prog_list'." 2178 } , 2179 2180 { 21, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2181 "add new text_install dir; move scripts_install txt files there", 2182 "Moved afni_fs_aparc+aseg_*.txt and demo*.niml.do there.\n" 2183 "This helps with the accuracy of 'make prog_list'." 2184 } , 2185 2186 { 21, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2187 "have programs return 0 on terminal options, like -help", 2188 "Adding: fat_mvm_gridconv.py." 2189 } , 2190 2191 { 20, Sep, 2018, RCR, "3dttest++", MICRO, TYPE_BUG_FIX, 2192 "fix copy-and-paste error for processing of voxelwise covariates", 2193 "Use of voxelwize covariates when only using -setA was crashing.\n" 2194 "Thanks to S. Kippenhan for noting the problem." 2195 } , 2196 2197 { 18, Sep, 2018, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2198 "outline BIDS-like analysis directory structure", 2199 "Add new DIRECTORY STRUCTURE NOTE section to -help output." 2200 } , 2201 2202 { 18, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2203 "have programs return 0 on terminal options, like -help", 2204 "Adding: FD2, Ifile, MakeColorMap, ScaleToMap, SurfMeasures, afni_run_R,\n" 2205 " balloon, imcat, inspec, myget, quickspec, qhull, rbox, qdelaunay." 2206 } , 2207 2208 { 17, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2209 "have programs return 0 on terminal options, like -help", 2210 "Adding: @auto_align, @djunct_4d_slices_to_3d_vol, @djunct_vol_3slice_select,\n" 2211 " @xyz_to_ijk, column_cat, get_afni_model_PRF.\n" 2212 "Bigger changes to Dimon, Dimon1." 2213 } , 2214 2215 { 14, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2216 "have programs return 0 on terminal options, like -help", 2217 "Adding: @Install_D99_macaque, @Install_NIH_Marmoset." 2218 } , 2219 2220 { 13, Sep, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2221 "have programs return 0 on terminal options, like -help", 2222 "So far: 3dSurf2Vol, 3dVol2Surf, 3dmaxima." 2223 } , 2224 2225 { 12, Sep, 2018, RCR, "3dClusterize.c", MICRO, TYPE_BUG_FIX, 2226 "fix limit check on -idat and -ithr; disable MMAP for input", 2227 NULL 2228 } , 2229 2230 { 10, Sep, 2018, RCR, "Makefile.INCLUDE", MICRO, TYPE_BUG_FIX, 2231 "add (copy of) Audio directory to afni_src.tgz build target", 2232 NULL 2233 } , 2234 2235 { 22, Aug, 2018, RCR, "tedana_wrapper.py", MINOR, TYPE_MODIFY, 2236 "change exec_or_error() to use afni_util.py, which returns strings", 2237 "Thanks to J Gonzalez-Castillo for noting this python3 update." 2238 } , 2239 2240 { 17, Aug, 2018, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_NEW_OPT, 2241 "add option -write_uvars_json; add a few more user vars", 2242 "Add afni_ver, afni_package and final_epi_dset to uvars.\n" 2243 "Add 'AFNI version' and 'AFNI package' to review basic output.\n" 2244 "Add afni_util:write_data_as_json(), lib_vars_object:get_attribute_dict()." 2245 } , 2246 2247 { 16, Aug, 2018, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_NEW_OPT, 2248 "add -show_computed_uvars; set template", 2249 NULL 2250 } , 2251 2252 { 15, Aug, 2018, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 2253 "added functions for extracting version information from dataset HISTORY", 2254 "E.g. get_last_history_ver_pack(), get_last_history_version().\n" 2255 "This file now depends on 're'." 2256 } , 2257 2258 { 14, Aug, 2018, RCR, "model_conv_PRF_6", MINOR, TYPE_BUG_FIX, 2259 "return a zero array on invalid parameters", 2260 "Thanks to E Silson for noting the problem." 2261 } , 2262 2263 { 13, Aug, 2018, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 2264 "actually apply opt -blur_opts_BIM", 2265 "Thanks to D Zhu for noting the problem." 2266 } , 2267 2268 { 7, Aug, 2018, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 2269 "if converting tedana.py results to standard space, include -space", 2270 "Thanks to L Dowdle for noting the problem." 2271 } , 2272 2273 { 24, Jul, 2018, RCR, "dcm2niix_afni", MAJOR, TYPE_ENHANCE, 2274 "version v1.0.20180622, including fix for enhanced DICOM Philips bvec/bval", 2275 "Update from C Rorden." 2276 } , 2277 2278 { 5, Jul, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2279 "add -mask_opts_automask", 2280 "Done for L Atlas." 2281 } , 2282 2283 { 5, Jul, 2018, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 2284 "use >! for writing rm.bpass.1D, in case of noclobber", 2285 "Thanks for D Handwerker for noting it." 2286 } , 2287 2288 { 2, Jul, 2018, RCR, "Makefile", MICRO, TYPE_MODIFY, 2289 "modify setup for Makefile.macos_10.12_local", 2290 "Use RLIB_CONVERT variable to apply libXm.a just for R_io.so." 2291 } , 2292 2293 { 22, Jun, 2018, RCR, "dcm2niix_afni", MAJOR, TYPE_ENHANCE, 2294 "version v1.0.20180614, including JPEG-LS support", 2295 "Update from C Rorden." 2296 } , 2297 2298 { 21, Jun, 2018, RCR, "get_afni_model_PRF_6_BAD", MICRO, TYPE_NEW_PROG, 2299 "wrapper for model Conv_PRF_6_BAD", 2300 "See model Conv_PRF_6_BAD in model_conv_PRF_6_BAD.c." 2301 } , 2302 2303 { 21, Jun, 2018, RCR, "model_PRF_6_BAD", MINOR, TYPE_NEW_PROG, 2304 "old model_PRF_6, but with version and gauss_file udpates", 2305 "This is for result comparison." 2306 } , 2307 2308 { 19, Jun, 2018, RCR, "model_conv_PRF_6", MINOR, TYPE_BUG_FIX, 2309 "fix rotation term, B should be 2*B", 2310 "Thanks to R Le, G Usabiaga and B Wandell for suggesting a review." 2311 } , 2312 2313 { 18, Jun, 2018, RCR, "model_conv_PRF_6", MINOR, TYPE_ENHANCE, 2314 "add AFNI_MODEL_PRF_GAUSS_FILE env var, to write image of Gaussian", 2315 "Done for model_conv_PRF and model_conv_PRF_6, should to _DOG, too." 2316 } , 2317 2318 { 18, Jun, 2018, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2319 "add build targets for get_afni_model_PRF/PRF_6", 2320 NULL 2321 } , 2322 2323 { 18, Jun, 2018, RCR, "afni-general", MINOR, TYPE_MODIFY, 2324 "more status 0 updates: file_tool, serial_helper", 2325 NULL 2326 } , 2327 2328 { 15, Jun, 2018, RCR, "afni-general", MINOR, TYPE_MODIFY, 2329 "update some programs so that -help is valid and return 0", 2330 "Update 3dGrayplot 3dresample 3dretroicor @2dwarper @FSlabel2dset tokens." 2331 } , 2332 2333 { 8, Jun, 2018, RCR, "3ddata.h", MICRO, TYPE_BUG_FIX, 2334 "have DUMP_MAT44 write to stdout again (might re-do stderr later)", 2335 "Need to fix align_epi_anat.py for stderr, but must check shell use.\n" 2336 "Thanks to T Radman for noting the problem." 2337 } , 2338 2339 { 6, Jun, 2018, RCR, "model_conv_PRF_6", MICRO, TYPE_MODIFY, 2340 "be clear that AFNI_MODEL_PRF_ON_GRID is not ready for this model", 2341 NULL 2342 } , 2343 2344 { 25, May, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2345 "add option -combine_opts_tedwrap, to pass to tedana_wrapper.py", 2346 "This is currently for passing -tedana_is_exec, say.\n" 2347 "Done for M Vaziri-Pashkam." 2348 } , 2349 2350 { 24, May, 2018, RCR, "@extract_meica_ortvec", MINOR, TYPE_ENHANCE, 2351 "remove any duplicates from merged lists", 2352 "The 4 categories (accepted/ignored, rejected/midk-rej) might not be\n" 2353 "a clean partition.\n" 2354 "Thanks to L Dowdle for noting the problem." 2355 } , 2356 2357 { 23, May, 2018, RCR, "get_afni_model_PRF", MINOR, TYPE_NEW_PROG, 2358 "this is just a wrapper for model parameter evaluation", 2359 "See model Conv_PRF in model_conv_PRF.c." 2360 } , 2361 2362 { 23, May, 2018, RCR, "get_afni_model_PRF_6", MINOR, TYPE_NEW_PROG, 2363 "this is just a wrapper for model parameter evaluation", 2364 "See model Conv_PRF_6 in model_conv_PRF_6.c." 2365 } , 2366 2367 { 23, May, 2018, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 2368 "add -ushort2float", 2369 "This will add the option to any to3d command via -gert_create_dataset.\n" 2370 "Done for H Brice." 2371 } , 2372 2373 { 18, May, 2018, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 2374 "handle '3dttest++ -Clustsim' files, with no blur", 2375 NULL 2376 } , 2377 2378 { 17, May, 2018, RCR, "3dNLfim", MICRO, TYPE_NEW_OPT, 2379 "add -help_models and -load_models", 2380 "This is easier than: '3dNLfim -DAFNI_MODEL_HELP_ALL=Y -signal eggs'." 2381 } , 2382 2383 { 16, May, 2018, RCR, "plug_vol2surf", MINOR, TYPE_NEW_OPT, 2384 "added map_all option for the main 'use vol2surf?' plugin menu", 2385 "The 'map_all' option applies plugin parameters to all mappable surfaces,\n" 2386 "rather than applying defaults to any surface not specified as surf_A/B.\n" 2387 "This allows one to use normals and the various mapping functions.\n" 2388 "Done for D Glen." 2389 } , 2390 2391 { 15, May, 2018, RCR, "tedana.py", MICRO, TYPE_NEW_OPT, 2392 "add --seed, update for modern numpy", 2393 "New option --seed can be used for regression testing.\n" 2394 "Use integer subscripts in arrays; replace some '== None' with 'is None'." 2395 } , 2396 2397 { 15, May, 2018, RCR, "tedana_wrapper.py", MICRO, TYPE_MODIFY, 2398 "back-port for python 2.6", 2399 "Use local check_output(), rather than from subprocess." 2400 } , 2401 2402 { 14, May, 2018, RCR, "afni.c", MICRO, TYPE_BUG_FIX, 2403 "check at 'only if do_css' should be css, not gss", 2404 "Without GLOBAL_SESSION, this blocked the All_Datasets session." 2405 } , 2406 2407 { 14, May, 2018, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2408 "add epi_anat as opt for -mask_apply; if tedana, suggest -blur_in_mask yes", 2409 NULL 2410 } , 2411 2412 { 14, May, 2018, RCR, "@stim_analyze_modern", MINOR, TYPE_NEW_PROG, 2413 "added this sample script to doc/misc_scripts", 2414 "This uses the advanced form of make_random_timing.py." 2415 } , 2416 2417 { 8, May, 2018, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 2418 "add multi-echo combine methods: OC_tedort, tedana_OC, tedana_OC_tedort", 2419 "With this, afni_proc.py can run tedana.py and extract projection\n" 2420 "components (projecting good orts from bad, making cleaner bad orts).\n" 2421 " OC_tedort : like AFNI's OC, but also regress clean orts\n" 2422 " tedana_OC : tedana.py's OC\n" 2423 " tedana_OC_tedort : tedana.py's OC, and regress clean orts\n" 2424 "The tedort (orthogonalized tedana projection components) terms are\n" 2425 "applied in the regress block, still as per-run terms." 2426 } , 2427 2428 { 8, May, 2018, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 2429 "3dQwarp warp datasets need only be named _WARP", 2430 "Thanks to dowdlelt on MB for bringing this up." 2431 } , 2432 2433 { 7, May, 2018, RCR, "@extract_meica_ortvec", MINOR, TYPE_NEW_OPT, 2434 "add -ver, -meica_dir, -work_dir, init history", 2435 NULL 2436 } , 2437 2438 { 7, May, 2018, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 2439 "EPI automask (full_mask) is no longer dilated by default", 2440 "Also, add -show_process_changes, to report changes affecting results." 2441 } , 2442 2443 { 3, May, 2018, RCR, "@extract_meica_ortvec", MINOR, TYPE_NEW_PROG, 2444 "new program to extract MEICA projection vectors", 2445 "These 'rejected' terms are orthogonalized to the 'accepted' ones.\n" 2446 "This was written to be called by afni_proc.py." 2447 } , 2448 2449 { 28, Apr, 2018, RCR, "3dSurf2Vol", MINOR, TYPE_NEW_OPT, 2450 "add option -stop_gap and map functions nzave, nzmode, median, nzmedian", 2451 NULL 2452 } , 2453 2454 { 25, Apr, 2018, RCR, "meica.py", MINOR, TYPE_BUG_FIX, 2455 "deal with numpy update that fails for 'array == None', use 'is None'", 2456 "Thanks to dowdlele on MB for noting this and pointing to the emdupre\n" 2457 "update on https://github.com/ME-ICA/me-ica." 2458 } , 2459 2460 { 25, Apr, 2018, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 2461 "python3 compatible as of version 1.0", 2462 NULL 2463 } , 2464 2465 { 24, Apr, 2018, RCR, "gen_epi_review.py", MINOR, TYPE_ENHANCE, 2466 "python3 compatible as of version 0.4", 2467 NULL 2468 } , 2469 2470 { 24, Apr, 2018, RCR, "auto_warp.py", MINOR, TYPE_ENHANCE, 2471 "python3 compatible as of version 0.4", 2472 NULL 2473 } , 2474 2475 { 23, Apr, 2018, RCR, "afni-general", MICRO, TYPE_MODIFY, 2476 "moved python_scripts/*.py down 1 level, under python_scripts/afni", 2477 "This is preparation for setup.py and __init__.py to install AFNI's\n" 2478 "python files using pip, and to then load them via 'module load afni'." 2479 } , 2480 2481 { 18, Apr, 2018, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 2482 "add -csim_show_clustsize and helper options to report cluster requirements", 2483 "Given a cluster table output by 3dClustSim, use this option to extract\n" 2484 "the mininum cluster size, given uncorrected and corrected p-values.\n" 2485 "Use -csim_pthr and -csim_alpha to specify those respective p-values." 2486 } , 2487 2488 { 16, Apr, 2018, RCR, "lib_afni1D.py", MICRO, TYPE_ENHANCE, 2489 "Afni1D: store array of comment lines in header; add show_header()", 2490 NULL 2491 } , 2492 2493 { 12, Apr, 2018, RCR, "3dMVM.R", MICRO, TYPE_NEW_OPT, 2494 "add -verb option", 2495 NULL 2496 } , 2497 2498 { 12, Apr, 2018, RCR, "dcm2niix_afni", MAJOR, TYPE_ENHANCE, 2499 "version v1.0.20180403, including support for Philips enhanced DICOMs", 2500 "Update from C Rorden." 2501 } , 2502 2503 { 5, Apr, 2018, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 2504 "always apply -regress_motion_per_run", 2505 NULL 2506 } , 2507 2508 { 4, Apr, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2509 "add -combine_opts_tedana, to pass opts down to tedana.py", 2510 NULL 2511 } , 2512 2513 { 4, Apr, 2018, RCR, "tedana_wrapper.py", MICRO, TYPE_ENHANCE, 2514 "allow for newlines in -tedana_opts; flush tedana.py command", 2515 NULL 2516 } , 2517 2518 { 4, Apr, 2018, RCR, "@update.afni.binaries", MICRO, TYPE_BUG_FIX, 2519 "set sysname early - forgot to commit this weeks ago...", 2520 NULL 2521 } , 2522 2523 { 3, Apr, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2524 "initial testing run with -combine_tedana_path", 2525 NULL 2526 } , 2527 2528 { 27, Mar, 2018, RCR, "make_random_timing.py", MICRO, TYPE_MODIFY, 2529 "modify help for sphinx formatting", 2530 NULL 2531 } , 2532 2533 { 26, Mar, 2018, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 2534 "modify defaults: VR base = MIN_OUTLIER, EPI/anat cost func = lpc+ZZ", 2535 NULL 2536 } , 2537 2538 { 7, Mar, 2018, RCR, "afni", MICRO, TYPE_BUG_FIX, 2539 "add do_css check around css access for making catenated session list", 2540 NULL 2541 } , 2542 2543 { 6, Mar, 2018, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2544 "okay, if macos and no .bash_profile, source .bashrc from .bash_profile", 2545 NULL 2546 } , 2547 2548 { 1, Mar, 2018, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 2549 "add -combine_method cases of OC_A and OC_B", 2550 NULL 2551 } , 2552 2553 { 1, Mar, 2018, RCR, "@compute_OC_weights", MINOR, TYPE_NEW_OPT, 2554 "add -oc_method (OC_A, OC_B)", 2555 "OC_B: compute T2* from full log() time series, rather than log(mean(TS))." 2556 } , 2557 2558 { 26, Feb, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2559 "add option -help_section, and use it to add some missing option help", 2560 NULL 2561 } , 2562 2563 { 23, Feb, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2564 "add option for running OC combine method, use '-combine_method OC'", 2565 "This will run the current method implemented in @compute_OC_weights.\n" 2566 "This is probably a bit of a test, as I expect to modify the base 'OC'\n" 2567 "method, and therefore add other related names." 2568 } , 2569 2570 { 23, Feb, 2018, RCR, "@compute_OC_weights", MINOR, TYPE_NEW_OPT, 2571 "add option -echo_times, for convenient use by afni_proc.py", 2572 NULL 2573 } , 2574 2575 { 22, Feb, 2018, RCR, "3dMean", MINOR, TYPE_NEW_OPT, 2576 "add option -weightset to compute a weighted sum", 2577 "This N-volume weight dataset is used to apply voxelwise weights to the N\n" 2578 "input datasets, one volumetric weight to each dataset. The motivated\n" 2579 "example is combining single runs (at a time) of multi-echo data with the\n" 2580 "weights generated by @compute_OC_weights." 2581 } , 2582 2583 { 21, Feb, 2018, RCR, "@compute_OC_weights", MICRO, TYPE_MODIFY, 2584 "apply T2* < 0 as limit", 2585 "Should have no effect on resulting weights, but make a prettier T2* map." 2586 } , 2587 2588 { 16, Feb, 2018, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 2589 "add option -mask_epi_anat, to apply tigher mask in place of full_mask", 2590 "By default, create epi_anat intersection mask." 2591 } , 2592 2593 { 16, Feb, 2018, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 2594 "add combine block and ability to process multi-echo data", 2595 "Have new options -dsets_me_echo and -dsets_me_run for input.\n" 2596 "Still need to implement OC and ME-ICA.\n" 2597 "Thanks to L Atlas and J Gonzalez-Castillo." 2598 } , 2599 2600 { 15, Feb, 2018, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 2601 "add showproc option to exec_tcsh_command(), to show command and text", 2602 NULL 2603 } , 2604 2605 { 15, Feb, 2018, RCR, "@compute_OC_weights", MAJOR, TYPE_NEW_PROG, 2606 "compute voxelwise weights for optimally combining multi-echo data", 2607 "The equations are based on the summer 2017 talk by J Gonzalez-Castillo." 2608 } , 2609 2610 { 13, Feb, 2018, RCR, "3dbucket", MICRO, TYPE_MODIFY, 2611 "return success of dataset write", 2612 NULL 2613 } , 2614 2615 { 1, Feb, 2018, RCR, "3dTto1D", MINOR, TYPE_NEW_OPT, 2616 "add methods 4095_count/frac/warn", 2617 "Count 4095 values, or warn if datum is short and max is 4095." 2618 } , 2619 2620 { 31, Jan, 2018, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 2621 "in MT2_event_list 'part', if no run events, output '* *'", 2622 "Done for W Tseng." 2623 } , 2624 2625 { 30, Jan, 2018, RCR, "make_random_timing.py", MICRO, TYPE_NEW_OPT, 2626 "add -help_concerns, to describe some general concerns regarding timing", 2627 NULL 2628 } , 2629 2630 { 26, Jan, 2018, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 2631 "applied various NeuroDebian patches from M Hanke and Y Halchenko", 2632 "Includes up_include_right, up_condition_dset_unload, up_3dNetCorrFix,\n" 2633 "and up-fix_inflate_compare.\n" 2634 "Thanks to M Hanke and Y Halchenko for the fixes." 2635 } , 2636 2637 { 26, Jan, 2018, RCR, "dicom_hinfo", MICRO, TYPE_BUG_FIX, 2638 "fix crash on no input file", 2639 NULL 2640 } , 2641 2642 { 10, Jan, 2018, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 2643 "also set PATH in .bash_profile, if it exists", 2644 NULL 2645 } , 2646 2647 { 2, Jan, 2018, RCR, "realtime_receiver.py", MINOR, TYPE_ENHANCE, 2648 "python3 compatible as of version 1.0", 2649 "Also, add -write_text_data for L Morris and D Huynh." 2650 } , 2651 2652 { 29, Dec, 2017, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 2653 "python3 compatible as of version 1.0", 2654 NULL 2655 } , 2656 2657 { 28, Dec, 2017, RCR, "uber_ttest.py", MINOR, TYPE_ENHANCE, 2658 "python3 compatible as of version 2.0", 2659 NULL 2660 } , 2661 2662 { 28, Dec, 2017, RCR, "gen_ss_review_table.py", MINOR, TYPE_ENHANCE, 2663 "python3 compatible as of version 1.0", 2664 NULL 2665 } , 2666 2667 { 27, Dec, 2017, RCR, "gen_group_command.py", MICRO, TYPE_ENHANCE, 2668 "python3 compatible as of version 1.0", 2669 NULL 2670 } , 2671 2672 { 27, Dec, 2017, RCR, "RetroTS.py", MICRO, TYPE_BUG_FIX, 2673 "prevent slice_order = 'Cutsom' case from wiping out passed order", 2674 "Thanks to J. Ho for noting the problem in the Matlab version." 2675 } , 2676 2677 { 22, Dec, 2017, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 2678 "add -select_runs and -mplaces", 2679 "For B Benson and A Harrewijn, see Example 18d." 2680 } , 2681 2682 { 19, Dec, 2017, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2683 "add -help for align_unifize_epi", 2684 NULL 2685 } , 2686 2687 { 19, Dec, 2017, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 2688 "uniq_list_as_dsets: (def) no restriction to prefix; dmUBLOCK known basis", 2689 NULL 2690 } , 2691 2692 { 12, Dec, 2017, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 2693 "added 'sample analysis script' to help (in GENERAL ANALYSIS NOTE)", 2694 NULL 2695 } , 2696 2697 { 11, Dec, 2017, RCR, "3dmask_tool", MICRO, TYPE_BUG_FIX, 2698 "in dilate, if pad but not convert, inset == dnew, so do not delete", 2699 "Thanks to nwlee (AFNI message board) for noting the problem." 2700 } , 2701 2702 { 10, Dec, 2017, RCR, "Dimon", MICRO, TYPE_ENHANCE, 2703 "apply -gert_to3d_prefix for GEMS I-files", 2704 "Done for M Kerich." 2705 } , 2706 2707 { 4, Dec, 2017, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 2708 "fix gtmax in case of global times and only 1 input dset", 2709 "This just lead to an inappropriate warning.\n" 2710 "Thanks to P Bedard for noting the problem." 2711 } , 2712 2713 { 30, Nov, 2017, RCR, "afni_base.py", MICRO, TYPE_BUG_FIX, 2714 "fix problems with relative path to root directory", 2715 "This affected afni_proc.py, for example, adding '/' in path names.\n" 2716 "Thanks to D Nielson for noting the problem." 2717 } , 2718 2719 { 27, Nov, 2017, RCR, "afni", MICRO, TYPE_BUG_FIX, 2720 "fix imseq.c: driven SAVE_MPEG offset by 1", 2721 NULL 2722 } , 2723 2724 { 27, Nov, 2017, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2725 "warn user for python version != 2.7 (3+ in particular)", 2726 NULL 2727 } , 2728 2729 { 21, Nov, 2017, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 2730 "add options -not_first and -not_last, to block tasks at run boundaries", 2731 "For C Smith." 2732 } , 2733 2734 { 15, Nov, 2017, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 2735 "-despike_mask had been tested with wrong option name", 2736 "Fix submitted by D Plunkett." 2737 } , 2738 2739 { 9, Nov, 2017, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 2740 "python3 compatible as of version 3.0", 2741 NULL 2742 } , 2743 2744 { 9, Nov, 2017, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 2745 "python3 compatible as of version 3.00", 2746 NULL 2747 } , 2748 2749 { 7, Nov, 2017, RCR, "afni_proc.py", MAJOR, TYPE_ENHANCE, 2750 "python3 compatible as of version 6.00", 2751 NULL 2752 } , 2753 2754 { 7, Nov, 2017, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 2755 "python3 compatible as of version 2.00", 2756 NULL 2757 } , 2758 2759 { 7, Nov, 2017, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 2760 "python3 compatible as of version 1.00", 2761 NULL 2762 } , 2763 2764 { 6, Nov, 2017, RCR, "afni-general", MAJOR, TYPE_ENHANCE, 2765 "first stab at making python program p2/p3 compatible", 2766 "Based on 2to3 and dglen mods, and tested in p2 and p3 environments." 2767 } , 2768 2769 { 1, Nov, 2017, RCR, "make_random_timing.py", MAJOR, TYPE_NEW_OPT, 2770 "implement the decay_fixed distribution type", 2771 "See make_random_timing.py -help_decay_fixed for details." 2772 } , 2773 2774 { 23, Oct, 2017, RCR, "3dDeconvolve", MICRO, TYPE_GENERAL, 2775 "add warnings if TR or run length is 0.0", 2776 NULL 2777 } , 2778 2779 { 20, Sep, 2017, RCR, "3dAutoTcorrelate", MICRO, TYPE_ENHANCE, 2780 "add help example", 2781 NULL 2782 } , 2783 2784 { 12, Sep, 2017, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 2785 "add -multi_timing_3col_tsv and -write_multi_timing", 2786 "Also, add -multi_show_duration_stats for married timing files.\n" 2787 "This is to process 3 column TSV (tab separated value) formatted timing\n" 2788 "files, as might be found in the OpenFMRI data." 2789 } , 2790 2791 { 12, Sep, 2017, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 2792 "modify main examples to use the lpc+ZZ cost function", 2793 NULL 2794 } , 2795 2796 { 11, Sep, 2017, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 2797 "if no regress block, omit gen_ss_review_scripts.py", 2798 NULL 2799 } , 2800 2801 { 6, Sep, 2017, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 2802 "re-apply cleaner xim use, so end of run signal has full image size", 2803 "Short end of run was hanging afni, but was not noticed since the\n" 2804 "communication was immediately terminated. Fixes multi-run use." 2805 } , 2806 2807 { 6, Sep, 2017, RCR, "plug_realtime", MINOR, TYPE_MODIFY, 2808 "allow user control of registration and plots with multi-chan/echo data", 2809 "This previously required channel merging or registering.\n" 2810 "For W Luh." 2811 } , 2812 2813 { 30, Aug, 2017, RCR, "model_conv_PRF", MICRO, TYPE_BUG_FIX, 2814 "determine NT restriction based on reorg", 2815 "Was limited to NT. Applies to PRF, PRF_6, PRF_DOG\n" 2816 "Thanks to E Silson for noting the problem." 2817 } , 2818 2819 { 30, Aug, 2017, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 2820 "add -fsl_timing_files and -write_as_married", 2821 "This is for converting FSL timing files to AFNI format." 2822 } , 2823 2824 { 22, Aug, 2017, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 2825 "add -apply_end_times_as_durations and -show_duration_stats", 2826 "For B Benson and P Vidal-Ribas." 2827 } , 2828 2829 { 18, Aug, 2017, RCR, "3dTto1D", MICRO, TYPE_MODIFY, 2830 "modify help", 2831 NULL 2832 } , 2833 2834 { 17, Aug, 2017, RCR, "3dcalc", MICRO, TYPE_MODIFY, 2835 "fix typos in help for minabove, maxbelow, acfwxm", 2836 "Thanks to A Wong for noting the minabove and maxbelow typos." 2837 } , 2838 2839 { 15, Aug, 2017, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2840 "test 3dClustSim as well, to check for OpenMP library linking", 2841 NULL 2842 } , 2843 2844 { 27, Jul, 2017, RCR, "3dNwarpApply", MICRO, TYPE_BUG_FIX, 2845 "fix memory alloc for warp file names", 2846 "Thanks to L Lebois (and others on MB) for noting the problem." 2847 } , 2848 2849 { 24, Jul, 2017, RCR, "nifti_tool", MINOR, TYPE_MODIFY, 2850 "treat ANALYZE more as NIFTI-1; apply more PRId64 macros for I/O", 2851 NULL 2852 } , 2853 2854 { 21, Jul, 2017, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 2855 "relative -bindir test needs quotes to block eval", 2856 NULL 2857 } , 2858 2859 { 19, Jul, 2017, RCR, "3dTto1D", MAJOR, TYPE_NEW_PROG, 2860 "time series to 1D : e.g. compute enorm, DVARS(RMS), SRMS", 2861 "Given time series data such as EPI or motion parameters, compute\n" 2862 "things like Euclidean norm and RMS (a.k.a. DVARS)." 2863 } , 2864 2865 { 19, Jul, 2017, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 2866 "adjust looking for good stim times to handle global timing", 2867 "Max time was previously that of the longest run. For global timing,\n" 2868 "accumulate across runs.\n" 2869 "Thanks to B Callaghan, Michael, ace327 and Jeff for noting the problem." 2870 } , 2871 2872 { 12, Jul, 2017, RCR, "afni_system_check.py", MICRO, TYPE_MODIFY, 2873 "ignore /opt/X11/lib/libXt.dylib check", 2874 "Undo Xt.7 and /opt/X11/lib/libXt.6.dylib checks." 2875 } , 2876 2877 { 11, Jul, 2017, RCR, "afni_system_check.py", MICRO, TYPE_MODIFY, 2878 "check if /opt/X11/lib/libXt.dylib points to Xt.6", 2879 "This is useless, pulling it out." 2880 } , 2881 2882 { 10, Jul, 2017, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 2883 "if -bindir is relative, require -no_recur", 2884 NULL 2885 } , 2886 2887 { 5, Jul, 2017, RCR, "3dAllineate", MICRO, TYPE_MODIFY, 2888 "make quieter: only report sub-brick messages if verbose", 2889 "Applied to 3dAllineate and 3dmerge." 2890 } , 2891 2892 { 28, Jun, 2017, RCR, "afni-general", MINOR, TYPE_GENERAL, 2893 "add afni_src/other_builds files for Fedora 25 (Makefile, OS_notes)", 2894 NULL 2895 } , 2896 2897 { 23, Jun, 2017, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 2898 "unalias grep; update cur_afni only when not abin", 2899 NULL 2900 } , 2901 2902 { 19, Jun, 2017, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 2903 "add -assume_dicom_mosaic to handle Siemens 3D format", 2904 "Done for A. Jahn." 2905 } , 2906 2907 { 16, Jun, 2017, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 2908 "check for libXt.7.dylib without flat_namespace", 2909 NULL 2910 } , 2911 2912 { 16, Jun, 2017, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2913 "add Makefile.linux_centos_7_64", 2914 "CentOS 7 and Ubuntu 16 will be new distribution build systems." 2915 } , 2916 2917 { 15, Jun, 2017, RCR, "uber_subject.py", MICRO, TYPE_BUG_FIX, 2918 "handle empty subj_dir", 2919 NULL 2920 } , 2921 2922 { 15, Jun, 2017, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2923 "add OS_notes.linux_centos_7.txt", 2924 NULL 2925 } , 2926 2927 { 15, Jun, 2017, RCR, "@SUMA_Make_Spec_FS", MICRO, TYPE_ENHANCE, 2928 "remove -f from top tcsh command; fix some bad tab indenting", 2929 NULL 2930 } , 2931 2932 { 5, Jun, 2017, RCR, "RetroTS.py", MINOR, TYPE_BUG_FIX, 2933 "peak_finder(): fix lengths of r['t'] and r['tR']", 2934 "Be more cautious with ratios that are very close to integers." 2935 } , 2936 2937 { 5, Jun, 2017, RCR, "RetroTS.py", MINOR, TYPE_BUG_FIX, 2938 "merge phase_base() fix by D Nielson", 2939 "range() is closed in matlab but half-open in python." 2940 } , 2941 2942 { 2, Jun, 2017, RCR, "afni-general", MINOR, TYPE_ENHANCE, 2943 "add Makefile.linux_ubuntu_16_64 and OS_notes.linux_ubuntu_16_64", 2944 "This is for setting up an Ubuntu 16 build machine." 2945 } , 2946 2947 { 30, May, 2017, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 2948 "add volreg params to enorm/outlier plot", 2949 NULL 2950 } , 2951 2952 { 30, May, 2017, RCR, "SUMA_IsoSurface", MICRO, TYPE_GENERAL, 2953 "remove non-ASCII characters in paper reference; remove tabs", 2954 NULL 2955 } , 2956 2957 { 26, May, 2017, RCR, "afni-general", MICRO, TYPE_ENHANCE, 2958 "add initial AFNI_digest_history.txt", 2959 NULL 2960 } , 2961 2962 { 25, May, 2017, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 2963 "can now apply -save_3dd_cmd and -make_3dd_contrasts in advanced case", 2964 "Advanced usage can generate 3dDeconvolve command scripts, with contrasts." 2965 } , 2966 2967 { 23, May, 2017, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 2968 "only warn 'ISI error: stimuli overlap' if olap > 0.0001", 2969 "Overlap could come from float->ascii->float conversion." 2970 } , 2971 2972 { 23, May, 2017, RCR, "suma", MICRO, TYPE_GENERAL, 2973 "warn on NULL glwDrawingAreaWidgetClass", 2974 NULL 2975 } , 2976 2977 { 17, May, 2017, RCR, "RetroTS.py", MICRO, TYPE_BUG_FIX, 2978 "D Nielson's fix in PeakFinder.py dealing with non-integer subscripts", 2979 "Required by latest version of numpy." 2980 } , 2981 2982 { 16, May, 2017, RCR, "meica.py", MICRO, TYPE_GENERAL, 2983 "cast floor/ceil functions to int when used as subscripts", 2984 "Required by latest version of numpy." 2985 } , 2986 2987 { 16, May, 2017, RCR, "meica.py", MINOR, TYPE_ENHANCE, 2988 "sync with https://bitbucket.org/prantikk/me-ica/src", 2989 "Update from version 2.5 beta9 to 2.5 beta11." 2990 } , 2991 2992 { 10, May, 2017, RCR, "model_conv_PRF_DOG", MINOR, TYPE_NEW_PROG, 2993 "new model: same as PRF, but Difference of Gaussians", 2994 "For E Silson and C Baker." 2995 } , 2996 2997 { 9, May, 2017, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 2998 "if to3d_prefix is NIFTI, clear write_as_nifti", 2999 "Thanks to A Nugent for noting the problem." 3000 } , 3001 3002 { 9, May, 2017, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 3003 "apply -offset for advanced case (remove from todo list)", 3004 NULL 3005 } , 3006 3007 { 2, May, 2017, RCR, "GIFTI", MINOR, TYPE_BUG_FIX, 3008 "properly handle column major order", 3009 "Convert to row major order on read; can control with gifti_tool.\n" 3010 "Thanks to JH Lee for noting the problem." 3011 } , 3012 3013 { 1, May, 2017, RCR, "@diff.files", MINOR, TYPE_NEW_OPT, 3014 "add option -diff_prog, to use something besides xxdiff", 3015 NULL 3016 } , 3017 3018 { 25, Apr, 2017, RCR, "GIFTI", MINOR, TYPE_MODIFY, 3019 "no COL_MAJOR changes for gifti_DA_rows_cols, write_*_file", 3020 "Also, init gifti_globs_t struct with verb=1." 3021 } , 3022 3023 { 25, Apr, 2017, RCR, "suma", MICRO, TYPE_MODIFY, 3024 "SUMA_input.c: 'r'ecord with oversample - use tcsh -c to delete files", 3025 "To be explicit about shell in system(), sending errors to /dev/null." 3026 } , 3027 3028 { 25, Apr, 2017, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 3029 "fix follower warps for gzipped NL-WARP datasets", 3030 "Thanks to C Connely for noting the problem." 3031 } , 3032 3033 { 25, Apr, 2017, RCR, "dcm2niix_afni", MICRO, TYPE_ENHANCE, 3034 "added to source for build testing", 3035 NULL 3036 } , 3037 3038 { 17, Apr, 2017, RCR, "1d_tool.py", MICRO, TYPE_MODIFY, 3039 "clarify source in -show_censored_trs (if Xmat, use header info)", 3040 NULL 3041 } , 3042 3043 { 12, Apr, 2017, RCR, "afni-general", MICRO, TYPE_MODIFY, 3044 "remove some non-ASCII chars: a couple of bad dashes and some Unicode", 3045 "some of the Unicode characters are upsetting sed via apsearch" 3046 } , 3047 3048 { 12, Apr, 2017, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 3049 "in suggest_best_prog_option(), do not search for -help, -h_* or similar", 3050 "A program without -help that tests it would otherwise lead to an\n" 3051 "infinitely recursive system call trying to use -help to suggest an option." 3052 } , 3053 3054 { 11, Apr, 2017, RCR, "@djunct_dwi_selector.bash", MICRO, TYPE_MODIFY, 3055 "if bad args, show usage and exit", 3056 "Else -help would open afni GUI and wait, hanging the build." 3057 } , 3058 3059 { 11, Apr, 2017, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 3060 "add GENERAL ANALYSIS NOTE; mentioned resting state scaling as optional", 3061 NULL 3062 } , 3063 3064 { 5, Apr, 2017, RCR, "uber_subject.py", MICRO, TYPE_BUG_FIX, 3065 "apply subject dir again; allow -cvar subj_dir to override default", 3066 NULL 3067 } , 3068 3069 { 5, Apr, 2017, RCR, "3dresample", MICRO, TYPE_MODIFY, 3070 "show -input as the typical usage, rather than -inset", 3071 NULL 3072 } , 3073 3074 { 3, Apr, 2017, RCR, "afni-general", MICRO, TYPE_MODIFY, 3075 "remove -f from @AddEdge, @DO.examples, @DriveAfni and @DriveSuma", 3076 "Since OS X is neglecting to pass DYLD variables to child shells,\n" 3077 "we need to rely on the rc files to reset them when driving GUIs." 3078 } , 3079 3080 { 30, Mar, 2017, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 3081 "allow subj_dir to affect the GUI (so no subject_results)", 3082 "Also, apply user command-line variables align_opts_aea and tlrc_opts_at\n" 3083 "(still not part of the GUI). Requested by J Rajendra." 3084 } , 3085 3086 { 30, Mar, 2017, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 3087 "run 3dclust -DAFNI_ORIENT=RAI to match SET_DICOM_XYZ coordinate order", 3088 "Suggested by J Rajendra." 3089 } , 3090 3091 { 27, Mar, 2017, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 3092 "NL warps of all-1 volume now uses -interp cubic for speed", 3093 "This applies only to interpolation of the warps via 3dNwarpApply.\n" 3094 "Also, use abs() in lists_are_same for -import_mask." 3095 } , 3096 3097 { 27, Mar, 2017, RCR, "@SUMA_Make_Spec_FS", MICRO, TYPE_GENERAL, 3098 "add comment about distortions for -NIFTI", 3099 NULL 3100 } , 3101 3102 { 27, Mar, 2017, RCR, "MapIcosahedron", MINOR, TYPE_NEW_OPT, 3103 "add -write_dist, for writing a distortion vector dataset", 3104 "After running something like:\n" 3105 " MapIcosahedron ... -write_dist test.dist\n" 3106 "to create test.dist.lh.sphere.reg.gii.txt, get summaries with:\n" 3107 " 1d_tool.py -collapse_cols euclidean_norm -show_mmms \\\n" 3108 " -infile test.dist.lh.sphere.reg.gii.txt" 3109 } , 3110 3111 { 21, Mar, 2017, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 3112 "allow for volreg-only script with MIN_OUTLIER", 3113 NULL 3114 } , 3115 3116 { 21, Mar, 2017, RCR, "MapIcosahedron", MINOR, TYPE_BUG_FIX, 3117 "fix projection of surfaces with non-zero centers", 3118 "Center each surface around 0,0,0 instead of leaving the offset in.\n\n" 3119 "Many thanks go to I Dewitt for even noticing this subtle issue,\n" 3120 "much less diagnosing where it might be coming from. Not easy." 3121 } , 3122 3123 { 21, Mar, 2017, RCR, "@FS_roi_label", MICRO, TYPE_BUG_FIX, 3124 "extra quote on line: choose one of $lbls", 3125 NULL 3126 } , 3127 3128 { 21, Mar, 2017, RCR, "@SUMA_Make_Spec_FS", MICRO, TYPE_ENHANCE, 3129 "add -verb to MapIcosahedron if script is in verbose mode", 3130 NULL 3131 } , 3132 3133 { 16, Mar, 2017, RCR, "RetroTS.py", MICRO, TYPE_MODIFY, 3134 "change peak_finder() to read data as floats", 3135 NULL 3136 } , 3137 3138 { 9, Mar, 2017, RCR, "afni-general", MICRO, TYPE_ENHANCE, 3139 "from D Warren: put exception handling around os.chmod calls", 3140 NULL 3141 } , 3142 3143 { 7, Mar, 2017, RCR, "RetroTS.py", MINOR, TYPE_BUG_FIX, 3144 "from J Zosky: default to using numpy.flipud()", 3145 "The flipud() function did not work in the original Matlab version,\n" 3146 "but it does in numpy. Use the new -legacy_transform opt for old\n" 3147 "(and presumably incorrect) results." 3148 } , 3149 3150 { 6, Mar, 2017, RCR, "RetroTS.py", MICRO, TYPE_MODIFY, 3151 "change -p and -v args to be read as floats; apply min(p/n_trace)", 3152 NULL 3153 } , 3154 3155 { 6, Mar, 2017, RCR, "AFNI.afnirc", MICRO, TYPE_BUG_FIX, 3156 "AFNI_COMPRESSOR can be set to GZIP, not gzip", 3157 NULL 3158 } , 3159 3160 { 3, Mar, 2017, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 3161 "add optimally combined 'Opt Comb' merge method", 3162 "Done with V Roopchansingh." 3163 } , 3164 3165 { 3, Feb, 2017, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 3166 "decay timing class now follows better distribution; new decay_old class", 3167 NULL 3168 } , 3169 3170 { 2, Feb, 2017, RCR, "steps_mac.rst", MINOR, TYPE_MODIFY, 3171 "rewrite OS X install instructions to use 10.7_local and fink", 3172 NULL 3173 } , 3174 3175 { 2, Feb, 2017, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 3176 "default mac package is now macosx_10.7_local", 3177 NULL 3178 } , 3179 3180 { 1, Feb, 2017, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 3181 "updates for fink and homebrew", 3182 NULL 3183 } , 3184 3185 { 27, Jan, 2017, RCR, "CA_EZ_atlas.csh", MICRO, TYPE_MODIFY, 3186 "with -help, do not dump TT_N27 in current directory", 3187 "Have script fail if any arguments are given (e.g. -help).\n" 3188 "Fix in all bin dirs and under atlases." 3189 } , 3190 3191 { 26, Jan, 2017, RCR, "Makefile.macosx_10.7_local", MINOR, TYPE_NEW_OPT, 3192 "this is a new Makefile to prep for exec directory dynamic linking", 3193 NULL 3194 } , 3195 3196 { 25, Jan, 2017, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 3197 "in 10.11+, check for DYLD variables via sub-shells", 3198 NULL 3199 } , 3200 3201 { 24, Jan, 2017, RCR, "align_epi_anat.py", MICRO, TYPE_ENHANCE, 3202 "trap failure from main 3dAllineate call", 3203 NULL 3204 } , 3205 3206 { 23, Jan, 2017, RCR, "make_random_timing.py", MICRO, TYPE_BUG_FIX, 3207 "allow automatic use of the INSTANT timing class", 3208 NULL 3209 } , 3210 3211 { 20, Jan, 2017, RCR, "make_random_timing.py", MAJOR, TYPE_ENHANCE, 3212 "advanced usage, program version 2.00", 3213 "Essentially a new program. The user may now define timing classes for\n" 3214 "stimulus and rest event types.\n" 3215 " see: make_random_timing.py -help_advanced\n" 3216 "Motivated by K Kircanski and A Stringaris." 3217 } , 3218 3219 { 19, Jan, 2017, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 3220 "fix for -final_anat", 3221 "Thanks to N Anderson for noting the problem." 3222 } , 3223 3224 { 19, Jan, 2017, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 3225 "advanced version 2 mostly ready", 3226 "Have -max_consec and -ordered_stimuli implemented in new version." 3227 } , 3228 3229 { 18, Jan, 2017, RCR, "3dmask_tool", MICRO, TYPE_MODIFY, 3230 "change example 3 to be with EPI masks", 3231 NULL 3232 } , 3233 3234 { 12, Jan, 2017, RCR, "afni_system_check.py", MICRO, TYPE_MODIFY, 3235 "for 10.11+, make flat warning and summary comment consistent", 3236 NULL 3237 } , 3238 3239 { 11, Jan, 2017, RCR, "make_random_timing.py", MICRO, TYPE_NEW_OPT, 3240 "added some help: -help_advanced, -help_todo", 3241 NULL 3242 } , 3243 3244 { 3, Jan, 2017, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 3245 "merged mrt branch into master - prep for advanced timing", 3246 NULL 3247 } , 3248 3249 { 29, Dec, 2016, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 3250 "remove case 16 (brainstem) from aparc+aseg.nii WM extraction in help", 3251 "Thanks to P Taylor for noting this." 3252 } , 3253 3254 { 15, Dec, 2016, RCR, "column_cat", MICRO, TYPE_ENHANCE, 3255 "allow for reading from stdin via either '-' or 'stdin'", 3256 NULL 3257 } , 3258 3259 { 9, Dec, 2016, RCR, "3dTsplit4D", MICRO, TYPE_ENHANCE, 3260 "allow for direct writing to NIFTI via prefix, e.g. result.nii", 3261 NULL 3262 } , 3263 3264 { 8, Dec, 2016, RCR, "3dTsplit4D", MINOR, TYPE_NEW_OPT, 3265 "add -digits and -keep_datum; other minor updates", 3266 NULL 3267 } , 3268 3269 { 8, Dec, 2016, RCR, "3dTsplit4D", MINOR, TYPE_NEW_PROG, 3270 "program to break 4D dataset into a set of 3D ones", 3271 "Authored by P Molfese." 3272 } , 3273 3274 { 8, Dec, 2016, RCR, "plug_vol2surf", MICRO, TYPE_ENHANCE, 3275 "add -cmask option to correspond with any auto non-zero mask", 3276 NULL 3277 } , 3278 3279 { 7, Dec, 2016, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 3280 "check for python2 and python3", 3281 NULL 3282 } , 3283 3284 { 5, Dec, 2016, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 3285 "allow *:1 (or *ANYTHING) to mean no event", 3286 "This is in case someone also marries empty run events.\n" 3287 "Done for R Kampe." 3288 } , 3289 3290 { 30, Nov, 2016, RCR, "afni-general", MAJOR, TYPE_ENHANCE, 3291 "<> range selector can now take a comma-delimited list of integers", 3292 "So for a dataset with integer values from 0 to 8, these commands\n" 3293 "should produce identical results:\n" 3294 " 3dcalc -a DSET+tlrc -expr 'a*amongst(a,3,4,5)' -prefix JELLO\n" 3295 " 3dbucket 'DSET+tlrc<4,3,5>' -prefix JELLO\n" 3296 " 3dbucket 'DSET+tlrc<3..5>' -prefix JELLO\n" 3297 " 3dbucket 'DSET+tlrc<2.3..5.86>' -prefix JELLO\n" 3298 "Of course, this will probably get further enhanced to a list of\n" 3299 "float ranges. We shall see.\n" 3300 "Comma-delimited labels should work now, with a plan to add general\n" 3301 "labels that might define all GM or similar in a FreeSurfer dataset, say." 3302 } , 3303 3304 { 18, Nov, 2016, RCR, "@Align_Centers", MICRO, TYPE_NEW_OPT, 3305 "add -prefix option, to name output", 3306 NULL 3307 } , 3308 3309 { 17, Nov, 2016, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 3310 "add some checks for flat_namespace on OS X", 3311 NULL 3312 } , 3313 3314 { 9, Nov, 2016, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 3315 "add -gert_chan_prefix", 3316 "Done for W Luh." 3317 } , 3318 3319 { 9, Nov, 2016, RCR, "to3d", MICRO, TYPE_MODIFY, 3320 "and Dimon/Dimon1: siemens timing outside range is only a warning", 3321 NULL 3322 } , 3323 3324 { 8, Nov, 2016, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 3325 "possibly invert slice order, as DICOM sorting might affect MRILIB_orients", 3326 "Thanks to W Luh for noting the problem." 3327 } , 3328 3329 { 2, Nov, 2016, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 3330 "handle 10.12 version string", 3331 NULL 3332 } , 3333 3334 { 1, Nov, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3335 "add PPI preparation options", 3336 "Add -regress_skip_censor to omit 3dD -censor option.\n" 3337 "Add -write_ppi_3dD_scripts with corresponding options\n" 3338 " -regress_ppi_stim_files and -regress_ppi_stim_labels.\n" 3339 "These make PPI pre and post regression scripts, along with\n" 3340 " the main analysis script.\n" 3341 "Done for S Haller." 3342 } , 3343 3344 { 24, Oct, 2016, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 3345 "bandpass notes and reference; stronger warning on missing -tlrc_dset", 3346 "Thanks to P Taylor." 3347 } , 3348 3349 { 20, Oct, 2016, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 3350 "check -mask_import for reasonable voxel dimensions", 3351 NULL 3352 } , 3353 3354 { 12, Oct, 2016, RCR, "RetroTS.py", MAJOR, TYPE_NEW_PROG, 3355 "distribute RetroTS.py (RetroTS.m converted to python)", 3356 "This should behave almost exactly as the MATLAB version.\n" 3357 "See 'RetroTS.py -help' for details.\n" 3358 "Much thanks to J Zosky for this contribution!" 3359 } , 3360 3361 { 11, Oct, 2016, RCR, "RetroTS.py", MICRO, TYPE_MODIFY, 3362 "make top-level executable, remove 'style' lib, quotes, use lib_RetroTS", 3363 NULL 3364 } , 3365 3366 { 9, Oct, 2016, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 3367 "new options -mask_import, -mask_intersect and -mask_union", 3368 "For J Stoddard and J Jarcho." 3369 } , 3370 3371 { 5, Oct, 2016, RCR, "afni-general", MAJOR, TYPE_NEW_PROG, 3372 "update from C Craddock and dclark87", 3373 "New Programs: 3dLFCD, 3dDegreeCentrality, 3dECM, 3dMSE, 3dsvm_linpredict." 3374 } , 3375 3376 { 28, Sep, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3377 "add -regress_ROI[_PC]_per_run options, to make per-run regressors", 3378 "Also, used 3dTproject to detrend PC regressors for appropriate censoring." 3379 } , 3380 3381 { 23, Sep, 2016, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 3382 "add -select_runs option", 3383 NULL 3384 } , 3385 3386 { 19, Sep, 2016, RCR, "@move.to.series.dirs", MICRO, TYPE_NEW_OPT, 3387 "add -glob, for processing glob forms via afni_util.py and xargs", 3388 NULL 3389 } , 3390 3391 { 19, Sep, 2016, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 3392 "add glob2stdout, for converting glob forms to lists in stdout", 3393 NULL 3394 } , 3395 3396 { 16, Sep, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3397 "add -radial_correlate option, to run @radial_correlate in proc script", 3398 NULL 3399 } , 3400 3401 { 16, Sep, 2016, RCR, "realtime_receiver.py", MICRO, TYPE_MODIFY, 3402 "continue even if requested GUI fails", 3403 NULL 3404 } , 3405 3406 { 13, Sep, 2016, RCR, "3dANOVA3", MICRO, TYPE_MODIFY, 3407 "change 'illegal argument after' errors to something more specific", 3408 NULL 3409 } , 3410 3411 { 13, Sep, 2016, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 3412 "add -blip_opts_qw to pass options to 3dQwarp in the blip block", 3413 NULL 3414 } , 3415 3416 { 29, Aug, 2016, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 3417 "add a few more DYLD_FALLBACK_LIBRARY_PATH tests", 3418 NULL 3419 } , 3420 3421 { 25, Aug, 2016, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 3422 "fix output.proc prefix in case -script has a path", 3423 "Also, allow -mask_apply group in the case of -tlrc_NL_warped_dsets.\n" 3424 "Thanks to C Capistrano and P Kim for noting the output.proc problem.\n" 3425 "Thanks to C Connolly for noting the mask problem." 3426 } , 3427 3428 { 25, Aug, 2016, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 3429 "add append flag to change_path_basename()", 3430 NULL 3431 } , 3432 3433 { 23, Aug, 2016, RCR, "file_tool", MINOR, TYPE_NEW_OPT, 3434 "add -fix_rich_quotes; if fixing a script, convert rich quotes to ASCII", 3435 "Done for G Chen." 3436 } , 3437 3438 { 22, Aug, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3439 "save all '3dAllineate -allcostX' anat/EPI costs to out.allcostX.txt", 3440 "This is another quality control measure." 3441 } , 3442 3443 { 19, Aug, 2016, RCR, "slow_surf_clustsim.py", MINOR, TYPE_ENHANCE, 3444 "can use surf_mask to restrict surface clustering", 3445 "Use '-uvar surf_mask' to restrict on_surface clustering to mask.\n" 3446 "Append SSCS command to end of script and handle NIFTI surf_vol.\n" 3447 "The surf_mask mas added for C Thomas." 3448 } , 3449 3450 { 16, Aug, 2016, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 3451 "look for new ACF/FWHM blur estimates", 3452 NULL 3453 } , 3454 3455 { 15, Aug, 2016, RCR, "afni_proc.py", MAJOR, TYPE_ENHANCE, 3456 "default clustsim method is now mixed model ACF", 3457 "This marks afni_proc.py version 5.00.\n" 3458 " o run 3dFWHMx with -ACF\n" 3459 " o ACF and ClustSim files go into sub-directories, files_ACF/ClustSim\n" 3460 " o -regress_run_clustsim now prefers arguments, ACF, FWHM, both, no\n" 3461 " o default clustsim method is now ACF (via -regress_run_clustsim yes)" 3462 } , 3463 3464 { 10, Aug, 2016, RCR, "afni-general", MICRO, TYPE_MODIFY, 3465 "in Makefile.INCLUDE, have afni depend first on libmri.a", 3466 NULL 3467 } , 3468 3469 { 6, Aug, 2016, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3470 "mri_read_ascii: check comment_buffer before strdup", 3471 NULL 3472 } , 3473 3474 { 5, Aug, 2016, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 3475 "make -help_install more current", 3476 NULL 3477 } , 3478 3479 { 5, Aug, 2016, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 3480 "add -marry_AM", 3481 "Added for J Wiggins." 3482 } , 3483 3484 { 1, Aug, 2016, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 3485 "do more hunting and reporting on libgomp and libglib", 3486 NULL 3487 } , 3488 3489 { 25, Jul, 2016, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 3490 "fixed attaching lone '-' to following label", 3491 "No NI_malloc might lead to crash, and the '-' was overwritten." 3492 } , 3493 3494 { 23, Jul, 2016, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 3495 "if empty regressor, check for -GOFORIT (only suggest if not found)", 3496 NULL 3497 } , 3498 3499 { 14, Jul, 2016, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3500 "THD_open_tcat: print error and return NULL on bad wildcard match", 3501 NULL 3502 } , 3503 3504 { 8, Jul, 2016, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 3505 "add -read_all, in case it is useful for sorting (e.g. -order_as_zt)", 3506 "Added for K Vishwanath." 3507 } , 3508 3509 { 7, Jul, 2016, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 3510 "add -order_as_zt to re-order from -time:tz to -time:zt", 3511 NULL 3512 } , 3513 3514 { 7, Jul, 2016, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 3515 "check for partial install of PyQt4 (might be common on OS X 10.11)", 3516 NULL 3517 } , 3518 3519 { 30, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3520 "allow single volume EPI input (e.g. to test blip correction)", 3521 "Also, auto -blip_forward_dset should come from tcat output." 3522 } , 3523 3524 { 29, Jun, 2016, RCR, "3dfim", MICRO, TYPE_BUG_FIX, 3525 "fix crash for dset open error with long dset name", 3526 "Thanks to J Henry for reporting the problem." 3527 } , 3528 3529 { 29, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3530 "can modify blip order; BLIP_BASE -> MEDIAN_BLIP; add BLIP_NOTE to help", 3531 NULL 3532 } , 3533 3534 { 27, Jun, 2016, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 3535 "allow for blip datasets that are not time series", 3536 NULL 3537 } , 3538 3539 { 24, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3540 "add -requires_afni_hist; warp vr_base to make final_epi dset", 3541 NULL 3542 } , 3543 3544 { 23, Jun, 2016, RCR, "plug_realtime", MICRO, TYPE_ENHANCE, 3545 "show pop-up if user selects Mask Vals without 3D RT registration", 3546 "Clarify this in the plugin Help. For L Li and V Roopchansingh." 3547 } , 3548 3549 { 23, Jun, 2016, RCR, "@auto_tlrc", MICRO, TYPE_ENHANCE, 3550 "allow to work with NIFTI template", 3551 NULL 3552 } , 3553 3554 { 22, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3555 "do nothing, but work really hard at it", 3556 "Rewrite EPI transformation steps by storing and applying an array\n" 3557 "of transformations: this should make future changes easier." 3558 } , 3559 3560 { 22, Jun, 2016, RCR, "@diff.tree", MICRO, TYPE_NEW_OPT, 3561 "added -diff_opts; e.g. -diff_opts -w", 3562 NULL 3563 } , 3564 3565 { 22, Jun, 2016, RCR, "@diff.files", MICRO, TYPE_NEW_OPT, 3566 "added -diff_opts; e.g. -diff_opts -w", 3567 NULL 3568 } , 3569 3570 { 22, Jun, 2016, RCR, "auto_warp.py", MICRO, TYPE_BUG_FIX, 3571 "correctly check base.exists()", 3572 NULL 3573 } , 3574 3575 { 17, Jun, 2016, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3576 "w/dglen, dsets with HEAD in prefix (but no suffix) could not be opened", 3577 NULL 3578 } , 3579 3580 { 16, Jun, 2016, RCR, "afni_proc.py", MAJOR, TYPE_ENHANCE, 3581 "EPI blip up/blip down distortion correction is ready", 3582 "Thanks to S Torrisi and D Glen." 3583 } , 3584 3585 { 16, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 3586 "if NLwarp but no EPI warp, no NL; fix refit of blip median datsets", 3587 "User probably forgot -volreg_tlrc_warp, so warn them." 3588 } , 3589 3590 { 14, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3591 "add -blip_forward_dset; if needed copy along any obliquity information", 3592 NULL 3593 } , 3594 3595 { 13, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3596 "add -align_unifize_epi : 3dUnifize EPI before anat alignment", 3597 "Thanks to D Glen and S Torrisi for suggesting it." 3598 } , 3599 3600 { 13, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3601 "add BLIP_BASE case for -volreg_align_to", 3602 "Use warped median forward blip volume as volreg alignment base." 3603 } , 3604 3605 { 10, Jun, 2016, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 3606 "add -blip_reverse_dset for blip up/blip down distortion correction", 3607 NULL 3608 } , 3609 3610 { 2, Jun, 2016, RCR, "afni-general", MINOR, TYPE_ENHANCE, 3611 "w/dglen: read num slices from Siemens 3D acquisition DICOM image files", 3612 NULL 3613 } , 3614 3615 { 1, Jun, 2016, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 3616 "minor updates to verbose output", 3617 NULL 3618 } , 3619 3620 { 23, May, 2016, RCR, "parse_fs_lt_log.py", MINOR, TYPE_NEW_PROG, 3621 "get an index list from a FreeSurfer labletable log file", 3622 NULL 3623 } , 3624 3625 3626 { 20, May, 2016, RCR, "afni_system_check.py", MINOR, TYPE_NEW_OPT, 3627 "add options -dot_file_list/_pack/_show", 3628 "List, package (tgz) or show the contents of found 'dot' files." 3629 } , 3630 3631 { 19, May, 2016, RCR, "dicom_hdr", MICRO, TYPE_BUG_FIX, 3632 "do not crash on missing input", 3633 NULL 3634 } , 3635 3636 { 5, May, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 3637 "-defaults similarly implies -do_dotfiles and apsearch yes", 3638 NULL 3639 } , 3640 3641 { 4, May, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 3642 "add -do_dotfiles and -do_extras", 3643 "Running apsearch and possibly editing dot files is only on request." 3644 } , 3645 3646 { 3, May, 2016, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 3647 "suggest -regress_est_blur_epits for resting state", 3648 "Thanks to S Torrisi for bringing up the question." 3649 } , 3650 3651 { 28, Apr, 2016, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 3652 "add -local_package, to use an already downloaded package", 3653 "Requested by P Taylor." 3654 } , 3655 3656 { 28, Apr, 2016, RCR, "3dMVM.R", MICRO, TYPE_MODIFY, 3657 "prevent any unexpected writing of dbg.AFNI.args files", 3658 "Only write such files given -dbg_args.\n" 3659 "Affects 1dRplot, 3dLME, 3dMEMA, 3dMVM, 3dPFM, 3dRprogDemo\n" 3660 " 3dSignatures, AFNIio, ExamineXmat, rPkgsInstall.\n" 3661 "The dbg files no longer start with '.'." 3662 } , 3663 3664 { 28, Apr, 2016, RCR, "afni-general", MICRO, TYPE_MODIFY, 3665 "add initial #!prog to tops of some meica programs, and bricks_test.sh", 3666 "This corresponds with -x permission clearing by yarikoptic." 3667 } , 3668 3669 { 27, Apr, 2016, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 3670 "prep for later: always extract volreg base, as vr_base*", 3671 NULL 3672 } , 3673 3674 { 26, Apr, 2016, RCR, "afni-general", MICRO, TYPE_MODIFY, 3675 "Makefile.INCLUDE: moved SCRIPTS into scripts_install", 3676 NULL 3677 } , 3678 3679 { 26, Apr, 2016, RCR, "tokens", MICRO, TYPE_ENHANCE, 3680 "handle arbitrarily long tokens", 3681 NULL 3682 } , 3683 3684 { 19, Apr, 2016, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 3685 "incorrectly reported 'IFM:RIF fatal error' for the case of no sorting", 3686 "Thanks to I Groen for reporting the problem." 3687 } , 3688 3689 { 18, Apr, 2016, RCR, "3dbucket", MICRO, TYPE_ENHANCE, 3690 "if THD_open_one_dataset fails, fall back to THD_open_dataset", 3691 "As with 3dTcat, fall back rather than failing outright." 3692 } , 3693 3694 { 18, Apr, 2016, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3695 "THD_open_tcat: fix wildcard input lacking sub-brick selectors", 3696 "Forgot to regenerate catenated list, dlocal." 3697 } , 3698 3699 { 15, Apr, 2016, RCR, "afni-general", MICRO, TYPE_ENHANCE, 3700 "added help macro CATENATE_HELP_STRING", 3701 "This displays a 'CATENATED AND WILDCARD DATASET NAMES' section in the\n" 3702 "help output from afni and 3dcalc (following 'INPUT DATASET NAMES')." 3703 } , 3704 3705 { 15, Apr, 2016, RCR, "NIFTI-2", MICRO, TYPE_MODIFY, 3706 "print int64_t using PRId64 macro, which looks ugly, but avoids warnings", 3707 NULL 3708 } , 3709 3710 { 8, Apr, 2016, RCR, "afni-general", MINOR, TYPE_ENHANCE, 3711 "auto-tcat inputs with spaces, wildcards and global selectors", 3712 "For example, input of 'DA*.HEAD DB*.HEAD DC*.HEAD[3,4]' would create\n" 3713 "a dataset with sub-bricks 3 and 4 from all D[ABC]*.HEAD datasets.\n" 3714 "If sub-brick selectors appear only at the end, they are global,\n" 3715 "otherwise they can be per input, as in 'DA*.HEAD[0,1] DB*.HEAD[2,3]'." 3716 } , 3717 3718 { 7, Apr, 2016, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 3719 "switch to have cjpeg depend on libjpeg.a, so it does not get rebuilt", 3720 NULL 3721 } , 3722 3723 { 7, Apr, 2016, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 3724 "add options -proto and -test_proto", 3725 "One can specify the download protocol as http, https or NONE." 3726 } , 3727 3728 { 5, Apr, 2016, RCR, "afni-general", MINOR, TYPE_ENHANCE, 3729 "THD_open_tcat works as wildcard - can apply sub-brick selectors", 3730 NULL 3731 } , 3732 3733 { 4, Apr, 2016, RCR, "3dTcat", MICRO, TYPE_ENHANCE, 3734 "if THD_open_one_dataset fails, fall back to THD_open_dataset", 3735 "Fall back rather than failing outright." 3736 } , 3737 3738 { 4, Apr, 2016, RCR, "THD_load_tcat", MINOR, TYPE_BUG_FIX, 3739 "set factors and labels at open time, not at load time", 3740 "This fixes use with 3dcalc and 3dinfo, though stats are not yet loaded." 3741 } , 3742 3743 { 31, Mar, 2016, RCR, "3dMVM.R", MICRO, TYPE_MODIFY, 3744 "do not create .dbg.AFNI.args files on -help usage", 3745 "Modified 1dRplot.R, 3dLME.R, 3dMEMA.R, 3dMVM.R, 3dPFM.R, 3dRprogDemo.R,\n" 3746 " 3dSignatures.R, ExamineXmat.R and rPkgsInstall.R." 3747 } , 3748 3749 { 30, Mar, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 3750 "possibly update .bashrc if .cshrc is updated", 3751 NULL 3752 } , 3753 3754 { 29, Mar, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_NEW_OPT, 3755 "add option -no_cert_verify, to skip server certificate verification", 3756 NULL 3757 } , 3758 3759 { 29, Mar, 2016, RCR, "gen_group_command.py", MICRO, TYPE_MODIFY, 3760 "3dMEMA no longer allows for a paied test", 3761 "One must now input contrast/stat from original regression." 3762 } , 3763 3764 { 29, Mar, 2016, RCR, "afni_restproc.py", MICRO, TYPE_MODIFY, 3765 "suggest that users consider afni_proc.py", 3766 "This was requested by Rayus." 3767 } , 3768 3769 { 26, Mar, 2016, RCR, "to3d", MICRO, TYPE_BUG_FIX, 3770 "another allowance for datasets exceeding 2 GB", 3771 "Thanks to SS Kim for noting the problem." 3772 } , 3773 3774 { 24, Mar, 2016, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 3775 "add option -use_obl_origin, to apply -oblique_origin to to3d command", 3776 "Also, run any to3d script via 'tcsh -x' so the users get to see." 3777 } , 3778 3779 { 22, Mar, 2016, RCR, "afni-general", MINOR, TYPE_ENHANCE, 3780 "modularize version checking", 3781 "Update .afni.vctime even if URL read fails, to not flood server." 3782 } , 3783 3784 { 21, Mar, 2016, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 3785 "get slightly more accurate motion ave via 3dTstat -nzmean", 3786 NULL 3787 } , 3788 3789 { 21, Mar, 2016, RCR, "3dANOVA", MICRO, TYPE_ENHANCE, 3790 "allow for up to 666 observations", 3791 "Consider changing this to use a string_list or something similar." 3792 } , 3793 3794 { 21, Mar, 2016, RCR, "GLTsymtest", MICRO, TYPE_NEW_OPT, 3795 "added -badonly, to avoid screen clutter from many good GLTs", 3796 NULL 3797 } , 3798 3799 { 21, Mar, 2016, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 3800 "run GLTsymtest on specified GLTs", 3801 NULL 3802 } , 3803 3804 { 15, Mar, 2016, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 3805 "-help_basis update: max convolved BLOCK() is ~5.1, not ~5.4", 3806 NULL 3807 } , 3808 3809 { 1, Mar, 2016, RCR, "GIFTI", MICRO, TYPE_BUG_FIX, 3810 "applied R Vincent fix for GIFTI datasets with Windows-style newlines", 3811 NULL 3812 } , 3813 3814 { 1, Mar, 2016, RCR, "tokens", MINOR, TYPE_NEW_PROG, 3815 "program to extract valid text entries from a file", 3816 NULL 3817 } , 3818 3819 { 29, Feb, 2016, RCR, "3dANOVA3", MICRO, TYPE_ENHANCE, 3820 "show prior options to any 'Unrecognized command line option'", 3821 "Added disp_strings() to libmri.a." 3822 } , 3823 3824 { 24, Feb, 2016, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 3825 "replace tlrc_no_ss with anat_has_skull toggle and move to anat block", 3826 NULL 3827 } , 3828 3829 { 24, Feb, 2016, RCR, "timing_tool.py", MINOR, TYPE_BUG_FIX, 3830 "fix -warn_tr_stats crash on empty timing file", 3831 "Thanks to Z Reagh for noting the problem." 3832 } , 3833 3834 { 19, Feb, 2016, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 3835 "add many tests and summarize potential issues", 3836 NULL 3837 } , 3838 3839 { 17, Feb, 2016, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 3840 "add function affine_to_params_6: where input is 12 element sub-matrix", 3841 NULL 3842 } , 3843 3844 { 16, Feb, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 3845 "add -ver and initial version reporting", 3846 NULL 3847 } , 3848 3849 { 10, Feb, 2016, RCR, "@ANATICOR", MICRO, TYPE_BUG_FIX, 3850 "fixed -radius option parsing", 3851 "Thanks to A Frithsen for noting the problem." 3852 } , 3853 3854 { 10, Feb, 2016, RCR, "afni-general", MICRO, TYPE_MODIFY, 3855 "full update to use https://afni.nimh.nih.gov (no longer http)", 3856 NULL 3857 } , 3858 3859 { 9, Feb, 2016, RCR, "@GradFlipTest", MICRO, TYPE_MODIFY, 3860 "trap for missing inputs (e.g. used with just -help)", 3861 NULL 3862 } , 3863 3864 { 9, Feb, 2016, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3865 "be sure isfinite is defined in FD2_inc.c, parser_int.c", 3866 NULL 3867 } , 3868 3869 { 8, Feb, 2016, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 3870 "access afni site via https protocol", 3871 NULL 3872 } , 3873 3874 { 5, Feb, 2016, RCR, "thd_niftiread", MICRO, TYPE_BUG_FIX, 3875 "NIFTI files with no *form_codes should default to +orig, not NIFTI_default", 3876 NULL 3877 } , 3878 3879 { 28, Jan, 2016, RCR, "3dMean", MICRO, TYPE_MODIFY, 3880 "fix help to correctly report -stdev as sqrt(var) {was var/(n-1)}", 3881 "Thanks to K Kerr (MB) for pointing out the mistake." 3882 } , 3883 3884 { 27, Jan, 2016, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 3885 "allow for tissue based regression with only regress block", 3886 NULL 3887 } , 3888 3889 { 4, Jan, 2016, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 3890 "add boundardy checks in get_1dcat_intlist and get_count_intlist", 3891 "Without the checks, using count or 1dcat as sub-brick selector method\n" 3892 "would lead to confusing crashes (if values exceeded #vols).\n" 3893 "Thanks to W Graves for reporting the problem." 3894 } , 3895 3896 { 3, Jan, 2016, RCR, "afni_system_check.py", MICRO, TYPE_MODIFY, 3897 "truncate 'top history' text for data trees", 3898 NULL 3899 } , 3900 3901 { 31, Dec, 2015, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 3902 "include AFNI_version_base.txt in build of afni_src.tgz", 3903 NULL 3904 } , 3905 3906 { 30, Dec, 2015, RCR, "afni-general", MAJOR, TYPE_ENHANCE, 3907 "w/DRG implement new version system", 3908 "See https://afni.nimh.nih.gov/pub/dist/MOTD/MOTD_2015_12_30.txt ." 3909 } , 3910 3911 { 29, Dec, 2015, RCR, "afni_system_check.py", MICRO, TYPE_BUG_FIX, 3912 "catch any empty directory listing from @FindAfniDsetPath", 3913 NULL 3914 } , 3915 3916 { 29, Dec, 2015, RCR, "@FindAfniDsetPath", MICRO, TYPE_MODIFY, 3917 "0 or bad # args returns 1 rather than 0", 3918 NULL 3919 } , 3920 3921 { 29, Dec, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 3922 "updated gitignore.src.txt and main 2 .gitignore files", 3923 NULL 3924 } , 3925 3926 { 28, Dec, 2015, RCR, "@diff.files", MICRO, TYPE_ENHANCE, 3927 "allow diffs to include existence of directories", 3928 NULL 3929 } , 3930 3931 { 19, Dec, 2015, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 3932 "removed CSFe from Example 10 of the help, to not lead people to use it", 3933 NULL 3934 } , 3935 3936 { 7, Dec, 2015, RCR, "MatAFNI_Demo.m", MICRO, TYPE_BUG_FIX, 3937 "merge fix from J. Pfannmoller", 3938 "Done with G Chen." 3939 } , 3940 3941 { 7, Dec, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 3942 "help update: modify example 11 to use SurfVol and add FREESURFER NOTE", 3943 NULL 3944 } , 3945 3946 { 17, Nov, 2015, RCR, "afni-general", MICRO, TYPE_GENERAL, 3947 "rename g_info to g_dicom_ctrl to avoid FreeBSD build conflict", 3948 "Thanks to J Bacon for noting the conflict." 3949 } , 3950 3951 { 6, Nov, 2015, RCR, "to3d", MICRO, TYPE_ENHANCE, 3952 "allow for single volumes beyond 2^31-1 bytes", 3953 "Done for Z Saad." 3954 } , 3955 3956 { 6, Nov, 2015, RCR, "@Align_Centers", MICRO, TYPE_NEW_OPT, 3957 "add option -cm_no_amask; like -cm but without -automask", 3958 NULL 3959 } , 3960 3961 { 4, Nov, 2015, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 3962 "add -slice_order_to_times", 3963 "This converts a list of slice indices (sorted by acq time)\n" 3964 "to slice times (ordered by index)." 3965 } , 3966 3967 { 28, Oct, 2015, RCR, "gen_ss_review_table.py", MICRO, TYPE_ENHANCE, 3968 "make 'a/E mask Dice coef' parent of 'mask correlation'", 3969 NULL 3970 } , 3971 3972 { 28, Oct, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 3973 "look for dice coef file ae_dice, as well ae_corr", 3974 NULL 3975 } , 3976 3977 { 28, Oct, 2015, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 3978 "output anat/EPI Dice coefficient, rather than correlation", 3979 NULL 3980 } , 3981 3982 { 28, Oct, 2015, RCR, "3ddot", MINOR, TYPE_NEW_OPT, 3983 "add -dodice, to get the Dice coefficient", 3984 NULL 3985 } , 3986 3987 { 26, Oct, 2015, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 3988 "compute TSNR restricted to uncensored TRs", 3989 NULL 3990 } , 3991 3992 { 26, Oct, 2015, RCR, "afni", MICRO, TYPE_MODIFY, 3993 "move version to show_AFNI_version and call on -ver", 3994 NULL 3995 } , 3996 3997 { 23, Oct, 2015, RCR, "afni", MICRO, TYPE_MODIFY, 3998 "move version output after some text requests", 3999 NULL 4000 } , 4001 4002 { 21, Oct, 2015, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 4003 "added -exec", 4004 NULL 4005 } , 4006 4007 { 25, Sep, 2015, RCR, "suma", MICRO, TYPE_MODIFY, 4008 "volume rendering is no longer the default for SUMA_VO_InitSlices", 4009 "So Do_06_VISdti_SUMA_visual_ex1.tcsh defaults to showing 3 volume slices." 4010 } , 4011 4012 { 24, Sep, 2015, RCR, "ccalc", MICRO, TYPE_MODIFY, 4013 "make dependency on libmri explicit", 4014 "Some of these operations are for building on Fedora 22." 4015 } , 4016 4017 { 24, Sep, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 4018 "inline func with static vars should be static", 4019 "Fails to link in Fedora 22." 4020 } , 4021 4022 { 24, Sep, 2015, RCR, "vol2surf", MICRO, TYPE_ENHANCE, 4023 "restrict THD_extract_series error messages (e.g. for RGB datasets)", 4024 "Requested by P Taylor." 4025 } , 4026 4027 { 24, Sep, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4028 "allow 3dD to proceed with only extra_stim_files", 4029 NULL 4030 } , 4031 4032 { 16, Sep, 2015, RCR, "suma", MICRO, TYPE_MODIFY, 4033 "w/dglen SUMA_find_any_object: fixed loss of isGraphDset result", 4034 NULL 4035 } , 4036 4037 { 11, Sep, 2015, RCR, "3dBandpass", MICRO, TYPE_MODIFY, 4038 "do not propagate scalars", 4039 NULL 4040 } , 4041 4042 { 11, Sep, 2015, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 4043 "edt_floatize.c: for NIFTI float->float with scale factors, apply them", 4044 "Also, fix determination of when to convert.\n" 4045 "Thanks to Pengmin (MB) for noting this problem." 4046 } , 4047 4048 { 10, Sep, 2015, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4049 "fix resulting aligned SurfVol if input is NIFTI", 4050 NULL 4051 } , 4052 4053 { 3, Sep, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 4054 "give REML priority in guessing stats_dset", 4055 NULL 4056 } , 4057 4058 { 2, Sep, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4059 "add -errts_dset to gen_ss_review_scripts.py command", 4060 NULL 4061 } , 4062 4063 { 2, Sep, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 4064 "some option vars were being over-written", 4065 NULL 4066 } , 4067 4068 { 2, Sep, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4069 "if rest and REML, use REML errts", 4070 NULL 4071 } , 4072 4073 { 1, Sep, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 4074 "track errts dset, and possibly use it for voxel dims", 4075 NULL 4076 } , 4077 4078 { 27, Aug, 2015, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 4079 "check for R packages via 'rPkgsInstall -pkgs ALL -check'", 4080 NULL 4081 } , 4082 4083 { 26, Aug, 2015, RCR, "Makefile.ptaylor.INCLUDE", MICRO, TYPE_ENHANCE, 4084 "put -L.. before $LFLAGS to link local libjpeg", 4085 NULL 4086 } , 4087 4088 { 25, Aug, 2015, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 4089 "if initial install, update .cshrc", 4090 "If initial install (afni not in PATH) and PATH not set in .cshrc,\n" 4091 "update path (PATH) and do 'apsearch -afni_help_dir' update in .cshrc." 4092 } , 4093 4094 { 21, Aug, 2015, RCR, "Makefile.INCLUDE", MICRO, TYPE_ENHANCE, 4095 "move gifti_tool/cifti_tool from EXPROGS to PROGRAM_LIST", 4096 "Modified 28 Makefiles." 4097 } , 4098 4099 { 21, Aug, 2015, RCR, "Makefile.INCLUDE", MICRO, TYPE_ENHANCE, 4100 "make cifti_tool", 4101 NULL 4102 } , 4103 4104 { 21, Aug, 2015, RCR, "cifti_tool", MAJOR, TYPE_NEW_PROG, 4105 "initial release: updated help and added -hist", 4106 "New program to evaluate CIFTI datasets." 4107 } , 4108 4109 { 21, Aug, 2015, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 4110 "start-of-run fix to -multi_timing_to_event_list offsets", 4111 NULL 4112 } , 4113 4114 { 21, Aug, 2015, RCR, "make_random_timing.py", MICRO, TYPE_ENHANCE, 4115 "add more help for 'NOTE: distribution of ISI', including a short script", 4116 NULL 4117 } , 4118 4119 { 20, Aug, 2015, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 4120 "add -show_isi_pdf and -show_isi_f_pdf", 4121 NULL 4122 } , 4123 4124 { 19, Aug, 2015, RCR, "gen_ss_review_table.py", MINOR, TYPE_NEW_OPT, 4125 "add -show_missing, to show all missing labels from all files", 4126 NULL 4127 } , 4128 4129 { 14, Aug, 2015, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 4130 "SUMA_CIFTI_2_edset: use 'no suma' version: SUMA_WriteDset_ns", 4131 NULL 4132 } , 4133 4134 { 13, Aug, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 4135 "megrged cifti-toy branch from Ziad, for viewing CIFTI dataset in suma", 4136 NULL 4137 } , 4138 4139 { 12, Aug, 2015, RCR, "@radial_correlate", MICRO, TYPE_NEW_OPT, 4140 "add -mask option, to apply instead of automask", 4141 "Done for Giri." 4142 } , 4143 4144 { 12, Aug, 2015, RCR, "gen_group_command.py", MINOR, TYPE_ENHANCE, 4145 "allow for generic/unknown commands via -command (e.g. ls, 3dTcat)", 4146 "Done for W-L Tseng." 4147 } , 4148 4149 { 7, Aug, 2015, RCR, "3dhistog", MICRO, TYPE_NEW_OPT, 4150 "add -noempty option, to ignore empty bins", 4151 NULL 4152 } , 4153 4154 { 7, Aug, 2015, RCR, "model_conv_PRF", MICRO, TYPE_MODIFY, 4155 "make everything static, to avoid confusion", 4156 NULL 4157 } , 4158 4159 { 7, Aug, 2015, RCR, "model_conv_PRF_6", MICRO, TYPE_BUG_FIX, 4160 "make everything static, to avoid confusion; proto for conv_set_ref", 4161 NULL 4162 } , 4163 4164 { 5, Aug, 2015, RCR, "nifti_tool", MICRO, TYPE_ENHANCE, 4165 "apply library updates for potentially writing NIFTI-2", 4166 NULL 4167 } , 4168 4169 { 5, Aug, 2015, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 4170 "if conversion to NIFTI-1 header fails on write, try NIFTI-2", 4171 NULL 4172 } , 4173 4174 { 5, Aug, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 4175 "add some support for reading Voxel_Bucket datasets into AFNI", 4176 "That is a type that is currently specific to SUMA." 4177 } , 4178 4179 { 3, Aug, 2015, RCR, "Dimon1", MICRO, TYPE_BUG_FIX, 4180 "fixed -drive_afni, -drive_wait and -rt_cmd command lists", 4181 NULL 4182 } , 4183 4184 { 3, Aug, 2015, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 4185 "applied ACQUSITION_TYPE as 3d+timing", 4186 "Slice timing was lost (by the plugin) in the change to 3d+t ACQ TYPE.\n" 4187 "Thanks to H Mandelkow for bringing this up." 4188 } , 4189 4190 { 3, Aug, 2015, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 4191 "added DTYPE_3DTM (3D+timing) ACQUSITION_TYPE", 4192 "Treats data as per volume, but with slice timing. This is needed for\n" 4193 "num_chan>0, but when data does not come in num_chan slices at a time." 4194 } , 4195 4196 { 31, Jul, 2015, RCR, "@FindAfniDsetPath", MICRO, TYPE_ENHANCE, 4197 "allow full paths to succeed ; no args gives help", 4198 NULL 4199 } , 4200 4201 { 30, Jul, 2015, RCR, "@auto_tlrc", MICRO, TYPE_BUG_FIX, 4202 "check for template existence even given path", 4203 "Was failing with -init_xform." 4204 } , 4205 4206 { 29, Jul, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 4207 "block any _REMLvar stats dset (was _REMLvar+)", 4208 "Might get stats*_REMLvar_nods, for example, via 3dREMLfit -dsort_nods." 4209 } , 4210 4211 { 29, Jul, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4212 "ANATICOR now works with task analysis, using -regress_reml_exec", 4213 "Done for R W Cox." 4214 } , 4215 4216 { 29, Jul, 2015, RCR, "3dcalc", MICRO, TYPE_MODIFY, 4217 "clarify error about mis-match in number of volumes", 4218 NULL 4219 } , 4220 4221 { 28, Jul, 2015, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 4222 "ANATICOR now includes zero volumes at censor points", 4223 "This matches non-ANATICOR and fast ANATICOR cases." 4224 } , 4225 4226 { 27, Jul, 2015, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 4227 "renamed -regress_WMeL_corr to -regress_make_corr_AIC and default to 'no'", 4228 NULL 4229 } , 4230 4231 { 24, Jul, 2015, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 4232 "GIFTI datasets should have NODE_INDEX list as first DataArray", 4233 "Thanks to N Oosterhof for pointing this out." 4234 } , 4235 4236 { 23, Jul, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 4237 "allow Graph_Bucket niml.dsets to be read, but just as 1D", 4238 NULL 4239 } , 4240 4241 { 17, Jul, 2015, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 4242 "Dimon->afni: small TCP buffers cause volumes to be passed slowly", 4243 "In iochan_recvall, increase nap time only if packets < 4K are received." 4244 } , 4245 4246 { 13, Jul, 2015, RCR, "nifti_tool", MAJOR, TYPE_ENHANCE, 4247 "nifti_tool is now based on NIFTI-2, with many corresponding new options", 4248 "The old nifti_tool (based on NIFTI-1) is now nifti1_tool." 4249 } , 4250 4251 { 13, Jul, 2015, RCR, "nifti1_tool", MINOR, TYPE_NEW_PROG, 4252 "nifti1_tool is the NIFTI-1 version of nifti_tool", 4253 NULL 4254 } , 4255 4256 { 13, Jul, 2015, RCR, "NIFTI-2", MAJOR, TYPE_ENHANCE, 4257 "added NIFTI-2 support into AFNI", 4258 "Main source update: nifti/nifti2 tree, then applied it in mostly\n" 4259 " thd_niftiread/write.c (plus gifti_io.h, 3ddata.h, mrilib.h).\n" 4260 "To compile into all of AFNI edit: Makefile.INCLUDE, SUMA_Makefile_NoDev,\n" 4261 " Makefile.avovk.INCLUDE and Makefile.ptaylor.INCLUDE." 4262 } , 4263 4264 { 11, Jul, 2015, RCR, "@diff.files", MICRO, TYPE_NEW_OPT, 4265 "added -longlist", 4266 NULL 4267 } , 4268 4269 { 1, Jul, 2015, RCR, "cifti_tool", MINOR, TYPE_NEW_OPT, 4270 "reorg and more recur functions", 4271 NULL 4272 } , 4273 4274 { 1, Jul, 2015, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 4275 "clarified help for -anat_unif_GM", 4276 NULL 4277 } , 4278 4279 { 24, Jun, 2015, RCR, "afni_xml_tool", MINOR, TYPE_NEW_OPT, 4280 "afni_xml updates, and start to afni_xml_tool", 4281 NULL 4282 } , 4283 4284 { 18, Jun, 2015, RCR, "3dExtrema", MINOR, TYPE_NEW_OPT, 4285 "added -nbest", 4286 "Output -nbest extrema; -quiet does not suppress extrema output." 4287 } , 4288 4289 { 17, Jun, 2015, RCR, "GIFTI", MINOR, TYPE_NEW_OPT, 4290 "added functions for reading from a buffer", 4291 NULL 4292 } , 4293 4294 { 16, Jun, 2015, RCR, "CIFTI", MINOR, TYPE_GENERAL, 4295 "added initial nifti/cifti tree", 4296 NULL 4297 } , 4298 4299 { 16, Jun, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4300 "applied -regress_stim_times_offset to typical timing files", 4301 "Allows for stim timing offset when copying to stimuli directory." 4302 } , 4303 4304 { 15, Jun, 2015, RCR, "nifti_tool", MINOR, TYPE_NEW_OPT, 4305 "added -disp_cext", 4306 NULL 4307 } , 4308 4309 { 10, Jun, 2015, RCR, "auto_warp.py", MICRO, TYPE_BUG_FIX, 4310 "clear any AFNI_COMPRESSOR variable, so that scripts do not get confused", 4311 "NIFTI is the default, so avoid script confusion with automatic nii.gz.\n" 4312 "In the future, maybe process as AFNI." 4313 } , 4314 4315 { 10, Jun, 2015, RCR, "NIFTI", MICRO, TYPE_BUG_FIX, 4316 "THD_open_one_dataset: let THD_open_nifti look for alternate files", 4317 "CHECK_FOR_DATA() requires a file name match, but NIFTI is forgiving." 4318 } , 4319 4320 { 10, Jun, 2015, RCR, "@diff.files", MAJOR, TYPE_NEW_PROG, 4321 "compare list of files with those in other directory", 4322 NULL 4323 } , 4324 4325 { 10, Jun, 2015, RCR, "@diff.tree", MAJOR, TYPE_NEW_PROG, 4326 "look for differences between files in two directories", 4327 "Should merge @diff.files and @diff.tree, and change to python." 4328 } , 4329 4330 { 8, Jun, 2015, RCR, "neuro_deconvolve.py", MICRO, TYPE_ENHANCE, 4331 "allow -inputs to include paths", 4332 NULL 4333 } , 4334 4335 { 6, Jun, 2015, RCR, "timing_tool.py", MICRO, TYPE_NEW_OPT, 4336 "added -per_run_file", 4337 NULL 4338 } , 4339 4340 { 2, Jun, 2015, RCR, "NIFTI", MICRO, TYPE_GENERAL, 4341 "NIFTI-1,2: added NIFTI_ECODE_CIFTI/VARIABLE_FRAME_TIMING/EVAL/MATLAB", 4342 NULL 4343 } , 4344 4345 { 1, Jun, 2015, RCR, "nifti_tool", MINOR, TYPE_ENHANCE, 4346 "diff/disp_hdr detects type; diff_hdr1/2", 4347 NULL 4348 } , 4349 4350 { 1, Jun, 2015, RCR, "3dttest++", MICRO, TYPE_NEW_OPT, 4351 "added -dupe_ok and more warnings when dataset labels match", 4352 NULL 4353 } , 4354 4355 { 27, May, 2015, RCR, "@Install_TSrestMovieDemo", MICRO, TYPE_BUG_FIX, 4356 "set and applied $demo as Suma_TSrestMovieDemo", 4357 NULL 4358 } , 4359 4360 { 26, May, 2015, RCR, "3dBlurToFWHM", MICRO, TYPE_MODIFY, 4361 "make -help output consistent in using FWHM (along with 3dLocalstat)", 4362 NULL 4363 } , 4364 4365 { 26, May, 2015, RCR, "NIFTI", MINOR, TYPE_ENHANCE, 4366 "nifti_read_header returns generic pointer; rename N-1/2 header read funcs", 4367 NULL 4368 } , 4369 4370 { 22, May, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4371 "help clarifications for -regress_ROI* options", 4372 NULL 4373 } , 4374 4375 { 22, May, 2015, RCR, "afni-general", MINOR, TYPE_MODIFY, 4376 "allow for small differences when comparing oblique angles", 4377 "Define OBLIQ_ANGLE_THRESH=0.01 as a tolerance for the difference.\n" 4378 "This was done to fix registration to external dset in realtime.\n" 4379 "Thanks to V Roopchansingh for bringing up the problem." 4380 } , 4381 4382 { 19, May, 2015, RCR, "3dClustSim", MICRO, TYPE_MODIFY, 4383 "do not allow -pthr to precede -both or -niml", 4384 "Otherwise -pthr values would be lost." 4385 } , 4386 4387 { 18, May, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4388 "allow ROI PC regression for local masks (not just external ones)", 4389 "External ROIs should now be passed via -anat_follower_ROI, rather than\n" 4390 "-regress_ROI_*, the latter no longer taking dataset parameters.\n" 4391 "Also changed -regress_ROI_erode to -anat_follower_erode and\n" 4392 "removed option -regress_ROI_maskave (use -regress_ROI)\n" 4393 "Done for R W Cox." 4394 } , 4395 4396 { 18, May, 2015, RCR, "gen_ss_review_table.py", MICRO, TYPE_NEW_OPT, 4397 "mention gen_ss_review_scripts.py -help_fields in help", 4398 NULL 4399 } , 4400 4401 { 8, May, 2015, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 4402 "added -regress_make_corr_vols", 4403 "Use this to compute average correlation volumes for various masks." 4404 } , 4405 4406 { 7, May, 2015, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 4407 "replaced slow 3dTfitter with 3dTproject in anaticor", 4408 "This should not affect the result, just the processing time." 4409 } , 4410 4411 { 5, May, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4412 "added help (inc Ex 11), follower modifications, WMe corr diag change", 4413 NULL 4414 } , 4415 4416 { 4, May, 2015, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 4417 "added -anat_follower, -anat_follower_ROI, -regress_anaticor_label", 4418 NULL 4419 } , 4420 4421 { 1, May, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 4422 "keep num regs of interest = 0 if num stim = 0", 4423 NULL 4424 } , 4425 4426 { 30, Apr, 2015, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 4427 "allow AM2 centering param via basis backdoor (for now)", 4428 "For example, use basis function 'BLOCK(2) :x:0.176'\n" 4429 "Done for J Britton." 4430 } , 4431 4432 { 29, Apr, 2015, RCR, "NIFTI", MINOR, TYPE_MODIFY, 4433 "allow reading and writing unknown extensions", 4434 NULL 4435 } , 4436 4437 { 28, Apr, 2015, RCR, "clib_02.nifti2", MINOR, TYPE_NEW_PROG, 4438 "added clib_02.nifti2.c demo and Makefile under nifti2 dir", 4439 NULL 4440 } , 4441 4442 { 28, Apr, 2015, RCR, "NIFTI", MAJOR, TYPE_ENHANCE, 4443 "apply updates to NIFTI-2 I/O library", 4444 "Also, include initial mods to nifti_tool, hidden under nifti2 dir." 4445 } , 4446 4447 { 28, Apr, 2015, RCR, "NIFTI", MINOR, TYPE_GENERAL, 4448 "add nifti/nifti2 directory with current NIFTI-1 versions of 4 files", 4449 "This tracks initial changes to nifti2_io.[ch] nifti_tool.[ch]." 4450 } , 4451 4452 { 24, Apr, 2015, RCR, "gen_group_command.py", MICRO, TYPE_ENHANCE, 4453 "tiny help update: examples of usage regarding subject IDs", 4454 NULL 4455 } , 4456 4457 { 23, Apr, 2015, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_NEW_OPT, 4458 "add -help_fields[_brief], to describe the 'basic' output fields", 4459 NULL 4460 } , 4461 4462 { 22, Apr, 2015, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 4463 "put in cat_matvec string to create warp.all.anat.aff12.1D", 4464 "Thanks to sgreen (MB) for noting the problem." 4465 } , 4466 4467 { 22, Apr, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4468 "add -todo; help update; verify use of erode list", 4469 NULL 4470 } , 4471 4472 { 22, Apr, 2015, RCR, "file_tool", MINOR, TYPE_ENHANCE, 4473 "add fix for non-unix files; allow for multiple tests with -prefix", 4474 NULL 4475 } , 4476 4477 { 22, Apr, 2015, RCR, "afni-general", MICRO, TYPE_MODIFY, 4478 "Makefile.linux_fedora_19_64: alter -I dirs for glib to build on F21", 4479 NULL 4480 } , 4481 4482 { 14, Apr, 2015, RCR, "uber_subject.py", MICRO, TYPE_NEW_OPT, 4483 "add MIN_OUTLIERS as an option for volreg base", 4484 NULL 4485 } , 4486 4487 { 14, Apr, 2015, RCR, "3dDeconvolve", MICRO, TYPE_MODIFY, 4488 "PLOT_matrix_gray: add error messages to clarify malloc failures", 4489 NULL 4490 } , 4491 4492 { 9, Apr, 2015, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4493 "fix -tlrc_NL_warped_dsets for NIFTI anat; add some -regress_ROI_PC help", 4494 NULL 4495 } , 4496 4497 { 8, Apr, 2015, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 4498 "updated to Ziad's new -revert option", 4499 NULL 4500 } , 4501 4502 { 8, Apr, 2015, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 4503 "check for FATCAT_DEMO", 4504 NULL 4505 } , 4506 4507 { 7, Apr, 2015, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4508 "TLRC_warped_dsets: no view update if type != BRIK", 4509 NULL 4510 } , 4511 4512 { 7, Apr, 2015, RCR, "afni_base.py", MICRO, TYPE_MODIFY, 4513 "ppves: no sel -> no quotes; dset_dims: check failures and return 4 vals", 4514 NULL 4515 } , 4516 4517 { 7, Apr, 2015, RCR, "3dnvals", MICRO, TYPE_MODIFY, 4518 "have 3dnvals return status 1 if all dataset opens fail", 4519 NULL 4520 } , 4521 4522 { 2, Apr, 2015, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 4523 "added -tlrc_NL_warped_dsets to import 3dQwarp result", 4524 "Added for P Molfese and others." 4525 } , 4526 4527 { 2, Apr, 2015, RCR, "rickr/Makefile", MICRO, TYPE_BUG_FIX, 4528 "Imon and serial_helper should not use LLIBS", 4529 NULL 4530 } , 4531 4532 { 1, Apr, 2015, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 4533 "anat followers and ROI_PC", 4534 "Datasets can follow the anatomical warps\n" 4535 "Added options -regress_ROI_PC, -regress_ROI_maskave, -regress_ROI_erode.\n" 4536 "PC allows for some number of principle components to be regressed, and\n" 4537 " maskave is for mask averages to be regressed.\n" 4538 "The _erode option applies to either, and happens before xform.\n" 4539 "Also, any anat with skull is applied as a follower.\n" 4540 "Also, -tcat_remove_first_trs can now take a list." 4541 } , 4542 4543 { 1, Apr, 2015, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 4544 "allow -censor_fill_parent with 2D files", 4545 NULL 4546 } , 4547 4548 { 31, Mar, 2015, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 4549 "allow -censor_fill_parent with simple 1D files", 4550 "Done for 3dpc and censoring in afni_proc.py." 4551 } , 4552 4553 { 30, Mar, 2015, RCR, "afni-general", MINOR, TYPE_ENHANCE, 4554 "update for selenium", 4555 "Includes: Makefile.linux_openmp*, xorg7*, osx_10.7*, fedora19_64,\n" 4556 "as well as Makefile.INCLUDE and rickr/Makefile for LLIBS." 4557 } , 4558 4559 { 23, Mar, 2015, RCR, "python-general", MINOR, TYPE_ENHANCE, 4560 "broke VarsObject class out into separate file", 4561 NULL 4562 } , 4563 4564 { 19, Mar, 2015, RCR, "unix_tutorial", MINOR, TYPE_ENHANCE, 4565 "populated AFNI_data6/unix_tutorial with Sphinx version", 4566 "The previous tutorial was moved under 'old'." 4567 } , 4568 4569 { 18, Mar, 2015, RCR, "sphinx", MAJOR, TYPE_ENHANCE, 4570 "added unix_tutorial to the doc tree", 4571 NULL 4572 } , 4573 4574 { 18, Mar, 2015, RCR, "sphinx", MICRO, TYPE_MODIFY, 4575 "renamed tutorials.rst to SelfGuidedScripts.rst, along with tag", 4576 NULL 4577 } , 4578 4579 { 18, Mar, 2015, RCR, "3dBandpass", MICRO, TYPE_ENHANCE, 4580 "let user know details of dimensionality reduction", 4581 NULL 4582 } , 4583 4584 { 13, Mar, 2015, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 4585 "added option -te_list to pass ECHO_TIMES to plug_realtime", 4586 NULL 4587 } , 4588 4589 { 13, Mar, 2015, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 4590 "added code to receive and store ECHO_TIMES", 4591 "This is passed as control information and is stored in rtin->TE." 4592 } , 4593 4594 { 13, Mar, 2015, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 4595 "added V Roopchansingh update for T2* est Merge function", 4596 NULL 4597 } , 4598 4599 { 12, Mar, 2015, RCR, "3dDeconvolve.py", MICRO, TYPE_MODIFY, 4600 "allow for collinearity in regressor warnings", 4601 NULL 4602 } , 4603 4604 { 12, Mar, 2015, RCR, "afni_base.py", MICRO, TYPE_BUG_FIX, 4605 "fixed capture in shell_exec2 for old python, where readlines() would hang", 4606 NULL 4607 } , 4608 4609 { 12, Mar, 2015, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 4610 "implemented fast=0 in get/show_process_stack", 4611 NULL 4612 } , 4613 4614 { 11, Mar, 2015, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 4615 "added covary and linear_fit; -listfunc takes -/stdin to read from stdin", 4616 NULL 4617 } , 4618 4619 { 3, Mar, 2015, RCR, "powell_int.c", MICRO, TYPE_BUG_FIX, 4620 "multiple include directives got joined on one line", 4621 NULL 4622 } , 4623 4624 { 3, Mar, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4625 "added MIN_OUTLER as an option to -volreg_align_to", 4626 "Also, updated requirement data from Feb 9 to Nov 9." 4627 } , 4628 4629 { 2, Mar, 2015, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4630 "fixed 3dTproject call for resting state on surface", 4631 "Thanks to Tara (message board) for noting the problem." 4632 } , 4633 4634 { 27, Feb, 2015, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 4635 "added -regress_WMeL_corr option, which I forgot about last time", 4636 NULL 4637 } , 4638 4639 { 27, Feb, 2015, RCR, "@compute_gcor", MICRO, TYPE_NEW_OPT, 4640 "added -corr_vol, to output a global correlation volume", 4641 "Note that afni_proc.py does these steps by default." 4642 } , 4643 4644 { 24, Feb, 2015, RCR, "neuro_deconvolve.py", MINOR, TYPE_ENHANCE, 4645 "re-wrote method: new decon, upsample, multiple files, reconvolve", 4646 "This is partially for evaluation of the decon/recon PPI steps." 4647 } , 4648 4649 { 13, Feb, 2015, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4650 "make WMeLocal for fast anaticor a float dataset", 4651 "Also, generate WMeL_corr as a diagnostic volume." 4652 } , 4653 4654 { 13, Feb, 2015, RCR, "3dcalc", MICRO, TYPE_ENHANCE, 4655 "allow for longer -prefix, to include what would be set via -session", 4656 "Done for P Kohn." 4657 } , 4658 4659 { 12, Feb, 2015, RCR, "make_stim_times.py", MICRO, TYPE_NEW_OPT, 4660 "added -no_consec option, to block consecutive events", 4661 NULL 4662 } , 4663 4664 { 12, Feb, 2015, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 4665 "added -regress_anaticor_fast/-regress_anaticor_fwhm", 4666 "This implements the 'fast' ANATICOR method, computing the WMeLocal\n" 4667 "voxel-wise regressors via an FWHM Gaussian sum of WMe voxels, rather\n" 4668 "than a uniform sum within a radius." 4669 } , 4670 4671 { 11, Feb, 2015, RCR, "model_conv_PRF", MICRO, TYPE_MODIFY, 4672 "use AFNI_MODEL_PRF_RAM_STATS to control RAM use reporting", 4673 "Maybe malloc_stats() is not available on macs." 4674 } , 4675 4676 { 10, Feb, 2015, RCR, "make_stim_times.py", MICRO, TYPE_MODIFY, 4677 "clarify use of both -nruns, -nt", 4678 NULL 4679 } , 4680 4681 { 9, Feb, 2015, RCR, "file_tool", MINOR, TYPE_ENHANCE, 4682 "warn on '\\' without preceding space", 4683 "Gang and J Rajendra ran into a problem on OS X 10.9.5." 4684 } , 4685 4686 { 9, Feb, 2015, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 4687 "applied updates matching 3dClustSim (9 table output)", 4688 "Output from 3dClustSim is now 9 tables: NN=1,2,3 by 1-,2-,bi-sided tests." 4689 } , 4690 4691 { 3, Feb, 2015, RCR, "model_conv_PRF", MINOR, TYPE_ENHANCE, 4692 "consolidate blur and reorg into one function, to reduce max memory usage", 4693 "This allows the program to run on weaker systems, cutting the max RAM\n" 4694 "usage by one half. A prior step was to allocate main RAM early so that\n" 4695 "free() would release to the OS (Linux), but that is now moot.\n" 4696 "This change has no effect on the results (no binary diff)." 4697 } , 4698 4699 { 28, Jan, 2015, RCR, "afni-general", MICRO, TYPE_ENHANCE, 4700 "in mri_fdrize, warn user if p->q is skipped because of < 20 voxels", 4701 NULL 4702 } , 4703 4704 { 28, Jan, 2015, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 4705 "take SurfMesh out of SUMA_PROGS; use LC_COLLATE in sort for prog_list", 4706 "done to keep GTS progs out of macosx_10.6_Intel_64.no.fink build" 4707 } , 4708 4709 { 20, Jan, 2015, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 4710 "added option -show_trs_to_zero, to compute length of iresp", 4711 "This is to computer the number of TRs until a curve bottoms out at 0." 4712 } , 4713 4714 { 20, Jan, 2015, RCR, "timing_tool.py", MICRO, TYPE_ENHANCE, 4715 "allow ',' as married timing separator (along with '*')", 4716 NULL 4717 } , 4718 4719 { 15, Jan, 2015, RCR, "@update.afni.binaries", MICRO, TYPE_NEW_OPT, 4720 "added -hist; if unknown opt and cur version, fail after check", 4721 NULL 4722 } , 4723 4724 { 15, Jan, 2015, RCR, "afni_skeleton.py", MICRO, TYPE_NEW_PROG, 4725 "just to save a starting point for other new programs", 4726 NULL 4727 } , 4728 4729 { 15, Jan, 2015, RCR, "afni_util.py", MICRO, TYPE_BUG_FIX, 4730 "fixed () in case of r(A,B,unbiased=1), which matches correlation_p()", 4731 NULL 4732 } , 4733 4734 { 15, Jan, 2015, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4735 "include -demean when running 3ddot on masks", 4736 NULL 4737 } , 4738 4739 { 15, Jan, 2015, RCR, "3ddot", MICRO, TYPE_ENHANCE, 4740 "explicitly state 'Pearson' correlation in help", 4741 NULL 4742 } , 4743 4744 { 14, Jan, 2015, RCR, "read_matlab_files.py", MINOR, TYPE_NEW_PROG, 4745 "read and possibly convert MATLAB files to 1D format", 4746 NULL 4747 } , 4748 4749 { 2, Jan, 2015, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 4750 "added MIN_OUTLIER to example 7", 4751 NULL 4752 } , 4753 4754 { 18, Dec, 2014, RCR, "afni_base.py", MICRO, TYPE_ENHANCE, 4755 "in shell_com:val(), if no stdout but have stderr, display stderr", 4756 NULL 4757 } , 4758 4759 { 10, Dec, 2014, RCR, "meica.py", MICRO, TYPE_BUG_FIX, 4760 "fixed 3dTshift input in case of --no_despike", 4761 "Thanks to M Plitt for the code fix." 4762 } , 4763 4764 { 2, Dec, 2014, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 4765 "-tlrc_NL_awpy_rm was not being applied", 4766 NULL 4767 } , 4768 4769 { 2, Dec, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 4770 "added floatscan to THD_load_nifti for case of double->float conversion", 4771 "Thanks to M Gregory." 4772 } , 4773 4774 { 25, Nov, 2014, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 4775 "added get_process_depth()", 4776 "sample use: afni_util.py -print 'get_process_depth()'" 4777 } , 4778 4779 { 21, Nov, 2014, RCR, "meica.py", MICRO, TYPE_MODIFY, 4780 "merged -affter into -nwarp in 5 3dNwarpApply calls", 4781 NULL 4782 } , 4783 4784 { 21, Nov, 2014, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 4785 "-anat_unifize_method none now means to skip, default means to do in AW", 4786 "Basically, this adds the ability to skip 3dUnifize completely." 4787 } , 4788 4789 { 19, Nov, 2014, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 4790 "do not allow num_suffix to be processed as octal", 4791 NULL 4792 } , 4793 4794 { 19, Nov, 2014, RCR, "3dclust", MICRO, TYPE_ENHANCE, 4795 "clarify -mni in help (do not use if already MNI)", 4796 NULL 4797 } , 4798 4799 { 10, Nov, 2014, RCR, "afni", MICRO, TYPE_ENHANCE, 4800 "added color maps Reds_and_Blues, and _w_Green", 4801 NULL 4802 } , 4803 4804 { 7, Nov, 2014, RCR, "mri_nwarp.c", MICRO, TYPE_BUG_FIX, 4805 "applied update to free temporary warp on behalf of RWC", 4806 NULL 4807 } , 4808 4809 { 7, Nov, 2014, RCR, "auto_warp.py", MICRO, TYPE_MODIFY, 4810 "moved -affter warp to -warp in 3dNwarpApply", 4811 NULL 4812 } , 4813 4814 { 7, Nov, 2014, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 4815 "moved -affter warp to -warp in 3dNwarpApply", 4816 "This applies the 22 Oct, 2014 change to 3dNwarpApply." 4817 } , 4818 4819 { 7, Nov, 2014, RCR, "model_conv_PRF_6", MINOR, TYPE_NEW_PROG, 4820 "6 parameter population receptive field estimate model", 4821 "Added sigrat (sigma ratio) and theta parameters.\n" 4822 "For E Silson and C Baker." 4823 } , 4824 4825 { 4, Nov, 2014, RCR, "CA_EZ_atlas.csh", MICRO, TYPE_MODIFY, 4826 "with unchecked -help this dumps TT_N27 in current directory", 4827 "Updated so that 'apearch -update_all_afni_help' does not dump dataset.\n" 4828 "Updated directly under pub/dist/bin.\n" 4829 "Should this script even be distributed?" 4830 } , 4831 4832 { 28, Oct, 2014, RCR, "timing_tool.py", MICRO, TYPE_ENHANCE, 4833 "expanded -help_basis", 4834 NULL 4835 } , 4836 4837 { 27, Oct, 2014, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 4838 "fixed strcmp trap in -sbns; have -sb_num_suffix look for any last integer", 4839 NULL 4840 } , 4841 4842 { 27, Oct, 2014, RCR, "afni-general", MINOR, TYPE_ENHANCE, 4843 "added 107 face images for 20 years", 4844 NULL 4845 } , 4846 4847 { 23, Oct, 2014, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 4848 "enhanced read_text_file and added shuffle_blocks", 4849 NULL 4850 } , 4851 4852 { 22, Oct, 2014, RCR, "3dmask_tool", MICRO, TYPE_BUG_FIX, 4853 "if padding for dilate/erode steps, preserve ijk_to_dicom_real", 4854 "Thanks to A Kurani for nothing the problem." 4855 } , 4856 4857 { 20, Oct, 2014, RCR, "imcat", MINOR, TYPE_BUG_FIX, 4858 "z and r: fixed y-padding", 4859 NULL 4860 } , 4861 4862 { 16, Oct, 2014, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 4863 "added sort_methods: none, acq_time, default, num_suffix, zposn", 4864 NULL 4865 } , 4866 4867 { 8, Oct, 2014, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 4868 "added -save_errors and more recovery chances, fixed sb_num_suffix app", 4869 "Stage 3 of sorting broke stage 2 of sorting.\n" 4870 "Thanks to V Roopchansingh for noting the problem." 4871 } , 4872 4873 { 25, Sep, 2014, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 4874 "fixed use of altered add_to_string_list()", 4875 "The changed usage broke options -drive_afni, -drive_wait and -rt_cmd.\n" 4876 "Thanks to V Roopchansingh for noting the problem." 4877 } , 4878 4879 { 24, Sep, 2014, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 4880 "added -list2 case under -listfunc", 4881 NULL 4882 } , 4883 4884 { 23, Sep, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 4885 "cat_strings was missing trailing byte", 4886 "Thanks to Q Li for noting the problem." 4887 } , 4888 4889 { 23, Sep, 2014, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 4890 "added some explicit -help and improved the few existing options", 4891 NULL 4892 } , 4893 4894 { 22, Sep, 2014, RCR, "3dexample1", MICRO, TYPE_ENHANCE, 4895 "made mention of 3dToyProg.c", 4896 NULL 4897 } , 4898 4899 { 22, Sep, 2014, RCR, "SUMA_Makefile_NoDev", MICRO, TYPE_MODIFY, 4900 "removed ../suma_*.o from clean directive", 4901 NULL 4902 } , 4903 4904 { 22, Sep, 2014, RCR, "thd_http.c", MICRO, TYPE_MODIFY, 4905 "changed mktemp() to mkstemp() to get rid of those compile warnings", 4906 NULL 4907 } , 4908 4909 { 22, Sep, 2014, RCR, "column_cat", MINOR, TYPE_BUG_FIX, 4910 "fixed implementation of -line, which messed up default operation", 4911 NULL 4912 } , 4913 4914 { 19, Sep, 2014, RCR, "3dexample1", MINOR, TYPE_NEW_PROG, 4915 "sample program to multiply a dataset by 2", 4916 "This is very basic example of reading/processing/writing AFNI datasets." 4917 } , 4918 4919 { 16, Sep, 2014, RCR, "3dmask_tool", MINOR, TYPE_NEW_OPT, 4920 "added -fill_dirs option, to specify directions for hole filling", 4921 "Added for D. Glen." 4922 } , 4923 4924 { 15, Sep, 2014, RCR, "file_tool", MINOR, TYPE_ENHANCE, 4925 "apply -prefix for -show_file_type (a dos2unix conversion)", 4926 NULL 4927 } , 4928 4929 { 10, Sep, 2014, RCR, "Dimon", MICRO, TYPE_ENHANCE, 4930 "handle num_chan > 1 in GERT_Reco scripts", 4931 NULL 4932 } , 4933 4934 { 8, Sep, 2014, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 4935 "round min dimension to 6 sig bits, then truncate to 3", 4936 "This helps catch cases where the dimension is just under\n" 4937 "some fairly 'round' number." 4938 } , 4939 4940 { 8, Sep, 2014, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 4941 "num_chan > 1 needs 3D+t ACQ type", 4942 "Thanks to V Roopchansingh for noting the problem." 4943 } , 4944 4945 { 8, Sep, 2014, RCR, "plug_realtime", MICRO, TYPE_BUG_FIX, 4946 "fixed free_PCOR_ivoxel_corr function call typos", 4947 "Thanks to Y Halchenko for noting the problem." 4948 } , 4949 4950 { 4, Sep, 2014, RCR, "r_idisp.o", MICRO, TYPE_MODIFY, 4951 "cast int64_t to long long to appease printf across multiple systems", 4952 NULL 4953 } , 4954 4955 { 3, Sep, 2014, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 4956 "merged in changes from C Craddock, with alterations", 4957 "This needs some more work." 4958 } , 4959 4960 { 2, Sep, 2014, RCR, "3dTcat", MICRO, TYPE_ENHANCE, 4961 "allow @filename format for -tpattern option", 4962 NULL 4963 } , 4964 4965 { 29, Aug, 2014, RCR, "slow_surf_clustsim.py", MICRO, TYPE_ENHANCE, 4966 "included blur in all help examples for clarity", 4967 NULL 4968 } , 4969 4970 { 28, Aug, 2014, RCR, "Dimon", MICRO, TYPE_ENHANCE, 4971 "test SOP IUID sorting", 4972 NULL 4973 } , 4974 4975 { 27, Aug, 2014, RCR, "3dcalc", MICRO, TYPE_ENHANCE, 4976 "applied AFNI_ORIENT for -LPI/-RAI", 4977 "Requested by Shane M. via the message board." 4978 } , 4979 4980 { 25, Aug, 2014, RCR, "gen_ss_review_table.py", MICRO, TYPE_BUG_FIX, 4981 "defined oind (for case that does not currently happen)", 4982 NULL 4983 } , 4984 4985 { 22, Aug, 2014, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 4986 "added -sort_method and -save_details", 4987 "Using the 'geme_index' sort method allows for real-time sorting\n" 4988 "of GE multi-echo data, before volumes are sent to 'afni'.\n" 4989 "Modification made for V Roopchansingh." 4990 } , 4991 4992 { 21, Aug, 2014, RCR, "model_conv_PRF", MICRO, TYPE_GENERAL, 4993 "minor details added to help output", 4994 NULL 4995 } , 4996 4997 { 13, Aug, 2014, RCR, "Dimon", MICRO, TYPE_GENERAL, 4998 "very minor update", 4999 NULL 5000 } , 5001 5002 { 12, Aug, 2014, RCR, "Dimon", MAJOR, TYPE_MODIFY, 5003 "this should basically work like the old version", 5004 "While no major change should be seen, this is an overhaul of\n" 5005 "the previous version, which should allow for realtime sorting." 5006 } , 5007 5008 { 12, Aug, 2014, RCR, "Dimon1", MINOR, TYPE_GENERAL, 5009 "Dimon1 is a fork of the previous working version of Dimon", 5010 "This can be a backup if there are troubles with the new Dimon." 5011 } , 5012 5013 { 12, Aug, 2014, RCR, "afni_system_check.py", MICRO, TYPE_GENERAL, 5014 "afni -ver is now only 1 line of output", 5015 NULL 5016 } , 5017 5018 { 5, Aug, 2014, RCR, "to3d", MICRO, TYPE_GENERAL, 5019 "added more comments about -ushort2float", 5020 "Requested by J Butman." 5021 } , 5022 5023 { 2, Aug, 2014, RCR, "make_stim_times.py", MINOR, TYPE_NEW_OPT, 5024 "added -run_trs, for cases when the TRs per run vary", 5025 "Requested on message board by Rebecca and later by Lisam." 5026 } , 5027 5028 { 15, Jul, 2014, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 5029 "output average motion per stim over response", 5030 "This will probably be replaced by averages over stimulus only time.\n" 5031 "Requested by D Pine." 5032 } , 5033 5034 { 15, Jul, 2014, RCR, "3dClustSim", MICRO, TYPE_GENERAL, 5035 "check for bad floats read for -fwhm[xyz]", 5036 "Requested by shanusmagnus." 5037 } , 5038 5039 { 11, Jul, 2014, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 5040 "fixed 1d_tool.py -pad_into_many_runs for bpass w/varying run lengths", 5041 "Thanks to d6anders for noting the problem." 5042 } , 5043 5044 { 3, Jul, 2014, RCR, "model_conv_PRF", MINOR, TYPE_BUG_FIX, 5045 "fixed a name space problem on macs", 5046 NULL 5047 } , 5048 5049 { 2, Jul, 2014, RCR, "afni-general", MICRO, TYPE_GENERAL, 5050 "added model_conv_PRF in Makefile.INCLUDE for distribution", 5051 NULL 5052 } , 5053 5054 { 27, Jun, 2014, RCR, "model_conv_PRF", MAJOR, TYPE_NEW_PROG, 5055 "population receptive field estimate model", 5056 "For E Silson and C Baker." 5057 } , 5058 5059 { 26, Jun, 2014, RCR, "3dresample", MINOR, TYPE_NEW_OPT, 5060 "added -bound_type FOV/SLAB option (FOV is orig and default)", 5061 "FOV preserves the field of view, SLAB preserves the SLAB\n" 5062 "(so with SLAB the extents should not change)" 5063 } , 5064 5065 { 26, Jun, 2014, RCR, "gen_ss_review_table.py", MICRO, TYPE_ENHANCE, 5066 "track 'degress of freedom' as 'degrees ...'", 5067 NULL 5068 } , 5069 5070 { 26, Jun, 2014, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 5071 "note any anat/EPI mask correlation value; correct 'degress' as 'degrees'", 5072 "Typo noted by J Stoddard." 5073 } , 5074 5075 { 26, Jun, 2014, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5076 "full_mask is now byte (via 3dmask_tool); note correlation with anat mask", 5077 NULL 5078 } , 5079 5080 { 25, Jun, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 5081 "removed SUMA/SUMA_MakeColorMap, SUMA/SUMA_MakeConsistent from source tree", 5082 "Thanks to Y Halchenko for bringing it up." 5083 } , 5084 5085 { 25, Jun, 2014, RCR, "to3d", MINOR, TYPE_ENHANCE, 5086 "allow -zorigin with x/y SLAB/FOV, particularly in case of nz==1", 5087 NULL 5088 } , 5089 5090 { 2, Jun, 2014, RCR, "slow_surf_clustsim.py", MICRO, TYPE_MODIFY, 5091 "niter defaults to 1000, to match recommendations and 'quick' example", 5092 NULL 5093 } , 5094 5095 { 30, May, 2014, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 5096 "if PREFIX ends in .nii, all saved datasets will be in NIFTI format", 5097 "Added for V Roopchansingh." 5098 } , 5099 5100 { 20, May, 2014, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5101 "macs: look for PyQt4 from homebrew and fink", 5102 NULL 5103 } , 5104 5105 { 19, May, 2014, RCR, "column_cat", MICRO, TYPE_NEW_OPT, 5106 "added -line option, e.g. to print only (0-based) line 17", 5107 NULL 5108 } , 5109 5110 { 16, May, 2014, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 5111 "changed default of -anat_unif_GM to no", 5112 "Use of -GM in 3dUnifiize was leading to some skull stripping failures.\n" 5113 "Thanks to J Stoddard for noting the problem." 5114 } , 5115 5116 { 16, May, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 5117 "make space in case compression programs have longer paths", 5118 "Thanks to D Thompson for finding the problematic code." 5119 } , 5120 5121 { 16, May, 2014, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5122 "a few updates:", 5123 " - if no AFNI binaries in path, try path to ASC.py\n" 5124 " - look for history files in data directories\n" 5125 " - print comments at end, so they are easier to notice" 5126 } , 5127 5128 { 13, May, 2014, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 5129 "allow for no stats dset", 5130 "With resting state and 3dTproject, afni_proc.py will not create stats." 5131 } , 5132 5133 { 12, May, 2014, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5134 "added -regress_use_tproject, and made the default=yes", 5135 "This will apply 3dTproject instead of 3dDeconvolve for resting\n" 5136 "state analysis. It is much faster, and creates the same result." 5137 } , 5138 5139 { 12, May, 2014, RCR, "3dTproject", MICRO, TYPE_ENHANCE, 5140 "allow for multiple -input dataset, without requiring quotes around them", 5141 NULL 5142 } , 5143 5144 { 12, May, 2014, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 5145 "-part_init 0 is not appropriate for -partition", 5146 "Text labels now apply, and the default is '-part_init INIT'." 5147 } , 5148 5149 { 9, May, 2014, RCR, "timing_tool.py", MICRO, TYPE_NEW_OPT, 5150 "added -part_init option; removed -chrono option", 5151 NULL 5152 } , 5153 5154 { 1, May, 2014, RCR, "@update.afni.binaries", MINOR, TYPE_BUG_FIX, 5155 "added -quick option; fixed recursive backups", 5156 NULL 5157 } , 5158 5159 { 29, Apr, 2014, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 5160 "micro fix to clarify 'initialization' help", 5161 "Thanks to Ziad for noting it" 5162 } , 5163 5164 { 29, Apr, 2014, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 5165 "update to run number display in case of -multi_timing_to_event_list", 5166 NULL 5167 } , 5168 5169 { 24, Apr, 2014, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 5170 "added -multi_timing_to_event_list", 5171 "This allows one to generate simple or details event lists, or to\n" 5172 "partition one event class by its predecessors.\n" 5173 "Partitioning added for W Tseng." 5174 } , 5175 5176 { 24, Apr, 2014, RCR, "afni_base.py", MICRO, TYPE_MODIFY, 5177 "shell_exec2() should always set so,se as arrays", 5178 NULL 5179 } , 5180 5181 { 24, Apr, 2014, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 5182 "changed use of nlines in limited_shell_exec()", 5183 NULL 5184 } , 5185 5186 { 24, Apr, 2014, RCR, "afni_history", MICRO, TYPE_BUG_FIX, 5187 "added proto for restrict_hlist()", 5188 NULL 5189 } , 5190 5191 { 16, Apr, 2014, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5192 "added MIN_OUTLIER parameter option for -volreg_base_dset", 5193 "Using '-volreg_base_dset MIN_OUTLIER' will result in the volume with\n" 5194 "the minimum outlier fraction to be extracted as the volreg base.\n" 5195 "Thanks to T Ross for the good suggestion, so long ago" 5196 } , 5197 5198 { 16, Apr, 2014, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 5199 "internal re-org, should have no effect", 5200 NULL 5201 } , 5202 5203 { 15, Apr, 2014, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 5204 "added optional 'pid' parameter to the get_process_stack() functions", 5205 NULL 5206 } , 5207 5208 { 10, Apr, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 5209 "@afni.run.me never made it into Makefile.INCLUDE for distribution", 5210 NULL 5211 } , 5212 5213 { 10, Apr, 2014, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5214 "added -index_to_run_tr, intended for use by afni_proc.py", 5215 NULL 5216 } , 5217 5218 { 9, Apr, 2014, RCR, "gen_ss_review_table.py", MAJOR, TYPE_NEW_PROG, 5219 "parse output from @ss_review_basic text into spreadsheet format", 5220 "This makes it easy to flag outlier subject values.\n" 5221 "Thanks to J Jarcho for encouragement." 5222 } , 5223 5224 { 9, Apr, 2014, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 5225 "give priority to GCOR files with 'out' in the name", 5226 NULL 5227 } , 5228 5229 { 4, Apr, 2014, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 5230 "fixed reading NIFTI obliquity w/dglen (lost Mar 22)", 5231 "Thanks to P Kundu for noting the problem." 5232 } , 5233 5234 { 31, Mar, 2014, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5235 "added -anat_unif_GM (def=yes); improved message for bad ricor input", 5236 NULL 5237 } , 5238 5239 { 31, Mar, 2014, RCR, "auto_warp.py", MICRO, TYPE_MODIFY, 5240 "some help text indentation and fix for display of non-string defaults", 5241 NULL 5242 } , 5243 5244 { 26, Mar, 2014, RCR, "auto_warp.py", MINOR, TYPE_BUG_FIX, 5245 "in 3dNwarpApply, use the base dataset as the -master, rather than WARP", 5246 "The WARP dataset is now often bigger, to handle warps to the dataset\n" 5247 "edges. The result from auto_warp.py should match the template/base.\n" 5248 "Note: the problem applies to binaries from 3/21 until 3/25 (now).\n" 5249 "Thanks to V Zachariou for noting the problem." 5250 } , 5251 5252 { 25, Mar, 2014, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5253 "added options -anat_uniform_method and -anat_opts_unif", 5254 "This correction may be particularly useful along with either\n" 5255 "-tlrc_NL_warp or -mask_segment_anat." 5256 } , 5257 5258 { 24, Mar, 2014, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5259 "added -regress_anaticor_radius", 5260 "This specifies the radius for the local white matter average.\n" 5261 "Option requested by S Torrisi." 5262 } , 5263 5264 { 21, Mar, 2014, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 5265 "if anaticor and censor, do not use keep_trs for blur est from errts", 5266 "Thanks to J Stoddard for noting the problem." 5267 } , 5268 5269 { 21, Mar, 2014, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 5270 "removed -e from 'tcsh -ef @ss_review_basic', for grep failures", 5271 "Macs terminate (correctly) when grep/wc return non-zero status, but\n" 5272 "Linux systems do not. Maybe tcsh authors did not like grep killing\n" 5273 "scripts, either...\n" 5274 } , 5275 5276 { 21, Mar, 2014, RCR, "afni_system_check.py", MINOR, TYPE_NEW_OPT, 5277 "added -data_root and enhancements for class data search", 5278 NULL 5279 } , 5280 5281 { 20, Mar, 2014, RCR, "1dUpsample", MINOR, TYPE_BUG_FIX, 5282 "fix reporting of file name in error messages; enhance said messages", 5283 NULL 5284 } , 5285 5286 { 14, Mar, 2014, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5287 "added some data and OS-specific tests", 5288 NULL 5289 } , 5290 5291 { 12, Mar, 2014, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5292 "set errts_pre in anaticor block; apply extends in blur no scale", 5293 NULL 5294 } , 5295 5296 { 11, Mar, 2014, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 5297 "added gen_ss_review_scripts.py command comment at bottom of _basic script", 5298 NULL 5299 } , 5300 5301 { 7, Mar, 2014, RCR, "afni", MICRO, TYPE_NEW_OPT, 5302 "added -no_detach, to prevent detaching from the terminal", 5303 "Useful since -DAFNI_DETACH=NO cannot work as written." 5304 } , 5305 5306 { 6, Mar, 2014, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 5307 "changed some censoring and per-stim behavior", 5308 "- if censoring, create X.stim.xmat.1D from uncensored matrix\n" 5309 "- if no censor, still report num regs of interest and TRs per stim\n" 5310 "- report per-stim censoring only with stim classes" 5311 } , 5312 5313 { 24, Feb, 2014, RCR, "realtime_receiver.py", MICRO, TYPE_ENHANCE, 5314 "added a little more detail to the demo example", 5315 NULL 5316 } , 5317 5318 { 20, Feb, 2014, RCR, "3dClustSim", MICRO, TYPE_BUG_FIX, 5319 "break WARNING_message(amesg) up, until W_m gets enhanced", 5320 "Strings applied via the format are limited to 16K." 5321 } , 5322 5323 { 19, Feb, 2014, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 5324 "if AM2 or IM, terminate extraction of ideals", 5325 "Ideal extraction should be done via 1d_tool.py, using the X-matrix." 5326 } , 5327 5328 { 19, Feb, 2014, RCR, "3dDeconvolve", MICRO, TYPE_ENHANCE, 5329 "warn if GLOBAL times and 1 early stim per run (looks local)", 5330 "An early stim means t <= (NT_r-1)*TR, where NT_r is #TRs in run r.\n" 5331 "Negative times are included, as they may be fillers for empty runs." 5332 } , 5333 5334 { 18, Feb, 2014, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 5335 "added -test_local_timing, to look for local vs. global timing issues", 5336 "- in some cases, promote married types to combine/compare them\n" 5337 "- keep track of '*' entries from timing files" 5338 } , 5339 5340 { 18, Feb, 2014, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 5341 "minor help update", 5342 NULL 5343 } , 5344 5345 { 10, Feb, 2014, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 5346 "show TRs per run, applied and censored", 5347 NULL 5348 } , 5349 5350 { 6, Feb, 2014, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 5351 "-help examples start with 'Example', for searching", 5352 NULL 5353 } , 5354 5355 { 3, Feb, 2014, RCR, "apsearch", MICRO, TYPE_NEW_OPT, 5356 "added -global_help/-gopts_help to print help for global options", 5357 NULL 5358 } , 5359 5360 { 15, Jan, 2014, RCR, "3dLRflip", MICRO, TYPE_BUG_FIX, 5361 "used bad filename without -prefix", 5362 "Var ext was not initialized." 5363 } , 5364 5365 { 14, Jan, 2014, RCR, "3dttest++", MICRO, TYPE_MODIFY, 5366 "make mask failure message more clear", 5367 "In THD_create_mask_from_string(), if string is short enough for a file\n" 5368 "check, report error with entire string." 5369 } , 5370 5371 { 14, Jan, 2014, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 5372 "added more system programs to check", 5373 NULL 5374 } , 5375 5376 { 30, Dec, 2013, RCR, "1d_tool.py", MICRO, TYPE_MODIFY, 5377 "skip polort against polort in -show_cormat_warnings", 5378 NULL 5379 } , 5380 5381 { 30, Dec, 2013, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 5382 "madd initial NT parametercw_malloc.c: moved mcw_malloc_dump_sort below _dump for solaris", 5383 "Apparently it does not like inconsistent declaration in same file,\n" 5384 "and mcw_malloc.h does not offer prototypes to many functions in the\n" 5385 "case of DONT_USE_MCW_MALLOC, including this one." 5386 } , 5387 5388 { 30, Dec, 2013, RCR, "file_tool", MINOR, TYPE_ENHANCE, 5389 "for -show_bad_backslash, check for '\\' as the last file character", 5390 "The fix (with -prefix) is to delete the last '\\' and end with a newline." 5391 } , 5392 5393 { 27, Dec, 2013, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 5394 "also output censored TRs per run, along with fractions", 5395 NULL 5396 } , 5397 5398 { 27, Dec, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5399 "added -show_tr_run_counts and -show_num_runs, for gen_ss_review_scripts.py", 5400 NULL 5401 } , 5402 5403 { 26, Dec, 2013, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 5404 "max and jump to cluster max are now based on masked dset, if possible", 5405 NULL 5406 } , 5407 5408 { 26, Dec, 2013, RCR, "3dBrickStat", MICRO, TYPE_MODIFY, 5409 "removed extra mask size output when using -mask option", 5410 "Text output is the intention of the program, so limit to requested text." 5411 } , 5412 5413 { 18, Dec, 2013, RCR, "@update.afni.binaries", MINOR, TYPE_MODIFY, 5414 "if system files seem to exist in the abin directory, block update", 5415 "If AFNI seems to be installed in a system directory (i.e. with OS level\n" 5416 "programs), default to not letting the update proceed. Options -sys_ok\n" 5417 "and -help_system_progs were added to provide control and details." 5418 } , 5419 5420 { 17, Dec, 2013, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 5421 "use -NEW by default with 3dDespike", 5422 "Added -despike_new to override the default behavior." 5423 } , 5424 5425 { 16, Dec, 2013, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_BUG_FIX, 5426 "fixed use of num_trs in the case of censoring", 5427 "Thanks to K Kerr for nothing the problem." 5428 } , 5429 5430 { 16, Dec, 2013, RCR, "auto_warp.py", MINOR, TYPE_NEW_OPT, 5431 "added -qblur option for P Molfese", 5432 NULL 5433 } , 5434 5435 { 9, Dec, 2013, RCR, "afni_util.py", MINOR, TYPE_BUG_FIX, 5436 "added backup function for get_process_stack", 5437 "BASE.shell_com() might return a short process list, probably from\n" 5438 "limited buffer space (for cmd.stdout)." 5439 } , 5440 5441 { 4, Dec, 2013, RCR, "@update.afni.binaries", MINOR, TYPE_BUG_FIX, 5442 "fixed ac++ condition and empty if", 5443 NULL 5444 } , 5445 5446 { 4, Dec, 2013, RCR, "afni_runme", MINOR, TYPE_NEW_PROG, 5447 "added this (Ziad's) script to sysadmin/scripts", 5448 NULL 5449 } , 5450 5451 { 3, Dec, 2013, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 5452 "added -prog_list for Ziad", 5453 NULL 5454 } , 5455 5456 { 12, Nov, 2013, RCR, "3dTfitter", MICRO, TYPE_ENHANCE, 5457 "added help example for PPI analysis", 5458 NULL 5459 } , 5460 5461 { 5, Nov, 2013, RCR, "@update.afni.binaries", MICRO, TYPE_BUG_FIX, 5462 "watch out of 'afni -ver' crashing because of missing libraries", 5463 "Trap check of $package, since it is included with $status.\n" 5464 "Thanks to CC Yen for noting the error." 5465 } , 5466 5467 { 5, Nov, 2013, RCR, "@FindAfniDsetPath", MICRO, TYPE_ENHANCE, 5468 "check AFNI_ATLAS_PATH and $HOME/.afni/atlases for datasets", 5469 NULL 5470 } , 5471 5472 { 1, Nov, 2013, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 5473 "OS X now defaults to 10.7_Intel package", 5474 NULL 5475 } , 5476 5477 { 1, Nov, 2013, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 5478 "let all-1 input for extents mask vary per run (for diff # TRs)", 5479 NULL 5480 } , 5481 5482 { 31, Oct, 2013, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 5483 "restrict blur estimation to uncensored TRs", 5484 NULL 5485 } , 5486 5487 { 31, Oct, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5488 "added -show_trs_run", 5489 "This will be used by afni_proc.py to restrict TRs for blur estimation\n" 5490 "to those that were not censored, per run." 5491 } , 5492 5493 { 30, Oct, 2013, RCR, "gen_group_command.py", MINOR, TYPE_ENHANCE, 5494 "added -keep_dirent_pre, to expand subject ID to directory entry prefix", 5495 "Requested by P Molfese." 5496 } , 5497 5498 { 24, Oct, 2013, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 5499 "output global correlation, and DoF info from review_basic", 5500 NULL 5501 } , 5502 5503 { 17, Oct, 2013, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 5504 "avoid infinite loop on empty SYM: or SYM: rows", 5505 NULL 5506 } , 5507 5508 { 30, Sep, 2013, RCR, "unix_tutorial", MINOR, TYPE_ENHANCE, 5509 "updates to installs/unix_commands/scripts/basic_*/bin/*", 5510 "These are for the 2 Dec 2013 bootcamp." 5511 } , 5512 5513 { 26, Sep, 2013, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 5514 "added more .h files to install_lib for compiling outside of afni_src", 5515 "Added rcmat.h, misc_math.h, thd_atlas.h, thd_ttatlas_query.h\n" 5516 "and thd_ttatlas_CA_EZ.h." 5517 } , 5518 5519 { 19, Sep, 2013, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5520 "allow regress_polort -1; added help for -regress_RSFC", 5521 NULL 5522 } , 5523 5524 { 19, Sep, 2013, RCR, "afni-general", MINOR, TYPE_MODIFY, 5525 "allow AFNI_COMPRESSOR to init decompression tool between gzip/pigz", 5526 NULL 5527 } , 5528 5529 { 19, Sep, 2013, RCR, "afni-general", MINOR, TYPE_NEW_OPT, 5530 "show label->sub-brick index conversion via AFNI_SHOW_LABEL_TO_INDEX", 5531 NULL 5532 } , 5533 5534 { 19, Sep, 2013, RCR, "afni", MINOR, TYPE_NEW_OPT, 5535 "added options -get_processed_env[_afni] and -global_opts", 5536 NULL 5537 } , 5538 5539 { 17, Sep, 2013, RCR, "mpeg_encode", MICRO, TYPE_MODIFY, 5540 "on fatal error, print message; added stdlib.h for free()/exit() protos", 5541 "Thanks to TheChymera (Message Board) for mentioning compile warnings." 5542 } , 5543 5544 { 13, Sep, 2013, RCR, "3dNLfim", MICRO, TYPE_BUG_FIX, 5545 "report an error instead of crashing if no -input is given", 5546 "This allows for getting individual signal help without the crash.\n" 5547 } , 5548 5549 { 13, Sep, 2013, RCR, "model_conv_cosine4", MICRO, TYPE_ENHANCE, 5550 "updated help with a usage example", 5551 NULL 5552 } , 5553 5554 { 12, Sep, 2013, RCR, "afni-general", MICRO, TYPE_GENERAL, 5555 "added SYSTEM_NAME to Makefile.linux_ubuntu_12_64", 5556 NULL 5557 } , 5558 5559 { 12, Sep, 2013, RCR, "afni-general", MINOR, TYPE_GENERAL, 5560 "added P Taylor's Makefile and install notes", 5561 "Makefile.linux_ubuntu_12_64, OS_notes.linux_ubuntu_12_64" 5562 } , 5563 5564 { 12, Sep, 2013, RCR, "afni-general", MINOR, TYPE_GENERAL, 5565 "added afni_src/other_builds directory", 5566 "This is for non-AFNI-build Makefiles and OS install notes.\n" 5567 "It has been initialized with:\n" 5568 " Makefile.linux_fedora_19_64\n" 5569 " OS_notes.linux_fedora_19_64.txt" 5570 } , 5571 5572 { 11, Sep, 2013, RCR, "model_conv_cosine4", MAJOR, TYPE_NEW_PROG, 5573 "A four half-cosine convolvable model.", 5574 "Based on: Fully Bayesian Spatio-Temporal Modeling of FMRI Data\n" 5575 " IEEE Transactions on Medical Imaging,\n" 5576 " Volume 23, Issue 2, February 2004, Pages 213-231\n" 5577 " Woolrich, M.W., Jenkinson, M., Brady, J.M., Smith, S.M.\n" 5578 "Requested by C Connolly and Felix." 5579 } , 5580 5581 { 3, Sep, 2013, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 5582 "Dimon -rt: if im_is_volume and single volume, get dz from image", 5583 "Thanks to A Nilsen for reporting the problem.\n" 5584 } , 5585 5586 { 26, Aug, 2013, RCR, "afni_system_check.py", MINOR, TYPE_NEW_OPT, 5587 "added -check_all, -find_prog, -casematch, -exact", 5588 "These changes are to add PATH searching for programs.\n" 5589 } , 5590 5591 { 20, Aug, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5592 "added -regress_RSFS, to run 3dRSFC", 5593 "Would run 3dRSFC per run on errts, to bandpass and compute parameters." 5594 } , 5595 5596 { 20, Aug, 2013, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 5597 "make 3dAutomask the default EPI strip method", 5598 "Suggested by D Glen. I should have done so in the first place." 5599 } , 5600 5601 { 20, Aug, 2013, RCR, "afni_system_check.py", MICRO, TYPE_ENHANCE, 5602 "update do search_path_dirs/show_found_in_path", 5603 NULL 5604 } , 5605 5606 { 14, Aug, 2013, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5607 "removed '_' from PYTHON_PATH; note any /sw/bin/python* files", 5608 NULL 5609 } , 5610 5611 { 14, Aug, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5612 "added non-linear standard space registration via -tlrc_NL_warp", 5613 NULL 5614 } , 5615 5616 { 2, Aug, 2013, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5617 "check for multiple R and python programs in PATH", 5618 NULL 5619 } , 5620 5621 { 2, Aug, 2013, RCR, "3dANOVA", MINOR, TYPE_BUG_FIX, 5622 "if AFNI_COMPRESSOR and input nii.gz, 'remove()' would not remove BRIK.gz", 5623 "Thanks to P Molfese for noting the problem." 5624 } , 5625 5626 { 1, Aug, 2013, RCR, "3dmask_tool", MINOR, TYPE_BUG_FIX, 5627 "fixed apparent pointer step issue, which happens on only some systems", 5628 "Apparent problem with MMAP (memory mapping of files).\n" 5629 "Thanks to W Gaggl for pointing out the problem." 5630 } , 5631 5632 { 1, Aug, 2013, RCR, "suma-general", MINOR, TYPE_BUG_FIX, 5633 "in suma_gifti.c, convert GIFTI's LPI to and from AFNI's RAI", 5634 "Done with Ziad. Thanks to N Oosterhof for bringing this up." 5635 } , 5636 5637 { 31, Jul, 2013, RCR, "3dmask_tool", MINOR, TYPE_BUG_FIX, 5638 "fixed failure to apply a negative dilation in non-convert case", 5639 "Thanks to W Gaggl for noting the problematic scenario." 5640 } , 5641 5642 { 22, Jul, 2013, RCR, "nifti_tool", MICRO, TYPE_GENERAL, 5643 "re-applied 2012 change of originator to shorts (lost with ITK update)", 5644 NULL 5645 } , 5646 5647 { 19, Jul, 2013, RCR, "afni-general", MINOR, TYPE_ENHANCE, 5648 "applied ITK compatibility updates from 11/2010 by H Johnson", 5649 NULL 5650 } , 5651 5652 { 19, Jul, 2013, RCR, "3dDeconvolve", MICRO, TYPE_ENHANCE, 5653 "no options implies -h", 5654 NULL 5655 } , 5656 5657 { 18, Jul, 2013, RCR, "@move.to.series.dirs", MINOR, TYPE_ENHANCE, 5658 "added -dprefix option, for output directory prefix", 5659 NULL 5660 } , 5661 5662 { 16, Jul, 2013, RCR, "afni_system_check.py", MINOR, TYPE_ENHANCE, 5663 "added checks for early python versions; added a little help", 5664 NULL 5665 } , 5666 5667 { 12, Jul, 2013, RCR, "suma", MICRO, TYPE_MODIFY, 5668 "return a good status (0) on -help", 5669 NULL 5670 } , 5671 5672 { 11, Jul, 2013, RCR, "afni_system_check.py", MINOR, TYPE_NEW_PROG, 5673 "perform many checks to validate a system for AFNI use", 5674 NULL 5675 } , 5676 5677 { 9, Jul, 2013, RCR, "Dimon", MINOR, TYPE_ENHANCE, 5678 "if unsigned shorts are detected, add -ushort2float to to3d command", 5679 NULL 5680 } , 5681 5682 { 9, Jul, 2013, RCR, "to3d", MINOR, TYPE_NEW_OPT, 5683 "added -ushort2float, for converting unsinged shorts to floats", 5684 "Requested by D Handwerker." 5685 } , 5686 5687 { 9, Jul, 2013, RCR, "file_tool", MINOR, TYPE_ENHANCE, 5688 "added more info for locating bad chars with -test", 5689 NULL 5690 } , 5691 5692 { 7, Jul, 2013, RCR, "@Install_FATCAT_DEMO", MINOR, TYPE_NEW_PROG, 5693 "replaces @Install_PTaylor_TractDemo", 5694 NULL 5695 } , 5696 5697 { 6, Jul, 2013, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 5698 "use NIFTI_INTENT_NONE for case of intent_code = FUNC_BUCK_TYPE", 5699 "3dbucket's FUNC_BUCK_TYPE went to intent_code for 1 vol dset" 5700 } , 5701 5702 { 1, Jul, 2013, RCR, "afni-general", MICRO, TYPE_NEW_OPT, 5703 "added AFNI_INCLUDE_HISTORY: set to No to omit history from output", 5704 NULL 5705 } , 5706 5707 { 28, Jun, 2013, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 5708 "added get/show_process_stack(), get/show_login_shell()", 5709 "Can use these from command line, e.g. :\n" 5710 " afni_util.py -eval 'show_login_shell()'\n" 5711 " afni_util.py -eval 'show_login_shell(verb=1)'\n" 5712 " afni_util.py -eval 'show_process_stack()'" 5713 } , 5714 5715 { 27, Jun, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5716 "added -regress_mot_as_ort", 5717 "Applies motion regressors via -ortvec, a potential future change." 5718 } , 5719 5720 { 25, Jun, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5721 "added -volreg_motsim and -volreg_opts_ms", 5722 NULL 5723 } , 5724 5725 { 14, Jun, 2013, RCR, "Makefile.NIH.openSUSE.11.4_64", MICRO, TYPE_ENHANCE, 5726 "added -fPIC to CCMIN (-fPIC is all over now, basically for R_io.so)", 5727 NULL 5728 } , 5729 5730 { 10, Jun, 2013, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 5731 "added -select_groups, -show_cormat, -volreg2allineate", 5732 NULL 5733 } , 5734 5735 { 10, Jun, 2013, RCR, "@simulate_motion", MINOR, TYPE_ENHANCE, 5736 "added warp_methods, etc.", 5737 NULL 5738 } , 5739 5740 { 31, May, 2013, RCR, "@simulate_motion", MAJOR, TYPE_NEW_PROG, 5741 "program to create time series simulated by motion parameters", 5742 NULL 5743 } , 5744 5745 { 17, May, 2013, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 5746 "added -f to curl, so that failures propagate to $status", 5747 NULL 5748 } , 5749 5750 { 14, May, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5751 "added options -show_argmin/max", 5752 NULL 5753 } , 5754 5755 { 13, May, 2013, RCR, "@RenamePanga", MINOR, TYPE_BUG_FIX, 5756 "added -column to count commands writing listfile", 5757 "There is a 4096 byte limit in addto_args(), which could be made dynamic." 5758 } , 5759 5760 { 10, May, 2013, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 5761 "named glob functions as afni_*; R was using sys funcs, rather than local", 5762 NULL 5763 } , 5764 5765 { 9, May, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5766 "added options -write_3dD_script and -write_3dD_prefix", 5767 NULL 5768 } , 5769 5770 { 8, May, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5771 "added options -rank, -rank_style, -reverse_rank", 5772 NULL 5773 } , 5774 5775 { 6, May, 2013, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5776 "added -regress_anaticor example; opt implies -mask_segment_anat/_erode", 5777 NULL 5778 } , 5779 5780 { 6, May, 2013, RCR, "3dinfo", MINOR, TYPE_NEW_OPT, 5781 "added option -slice_timing", 5782 NULL 5783 } , 5784 5785 { 6, May, 2013, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 5786 "added option -transpose_write", 5787 NULL 5788 } , 5789 5790 { 3, May, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5791 "added options -regress_anaticor and -mask_segment_erode", 5792 "Use the -regress_anaticor option to regress the WMeLocal time series.\n" 5793 "This is the ANATICOR method of HJ Jo." 5794 } , 5795 5796 { 1, May, 2013, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 5797 "added -help example for -show_trs_uncensored", 5798 NULL 5799 } , 5800 5801 { 29, Apr, 2013, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 5802 "set AFNI_NO_OBLIQUE_WARNING in scripts", 5803 NULL 5804 } , 5805 5806 { 26, Apr, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5807 "added -show_trs_censored/_uncensored (mostly for X-matrix datasets)", 5808 NULL 5809 } , 5810 5811 { 24, Apr, 2013, RCR, "@move.to.series.dirs", MINOR, TYPE_NEW_PROG, 5812 "partition a list of DICOM files by series number", 5813 "Done for I Shapira." 5814 } , 5815 5816 { 24, Apr, 2013, RCR, "3dinfo", MINOR, TYPE_BUG_FIX, 5817 "allow -space for nifti; actually exit if -view and result exists", 5818 "Thanks to I Schwabacher for noting the problem and fix." 5819 } , 5820 5821 { 24, Apr, 2013, RCR, "@2dwarper.Allin", MINOR, TYPE_BUG_FIX, 5822 "did not set 'ver' before goto START", 5823 "Thanks to I Schwabacher for noting the problem and fix." 5824 } , 5825 5826 { 24, Apr, 2013, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 5827 "added -censor_next_TR", 5828 "Sticking with backward diff for deriv, as it makes sense for censoring." 5829 } , 5830 5831 { 23, Apr, 2013, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 5832 "added eroded ROIs for -regress_ROI: WMe, GMe, CSFe", 5833 NULL 5834 } , 5835 5836 { 22, Apr, 2013, RCR, "auto_warp.py", MINOR, TYPE_GENERAL, 5837 "modified afni_base.afni_name.new() with 2 cases of parse_pref=1", 5838 "This is currently the only application of that parameter." 5839 } , 5840 5841 { 17, Apr, 2013, RCR, "3dAFNItoNIFTI", MINOR, TYPE_BUG_FIX, 5842 "fixed old use of use of strcat() after strdup()", 5843 "Thanks to B Benson and J Stoddard for noting the problem." 5844 } , 5845 5846 { 16, Apr, 2013, RCR, "3dmaskave", MINOR, TYPE_NEW_OPT, 5847 "added -sumsq (sum squares) and -enorm (Euclidean norm) options", 5848 NULL 5849 } , 5850 5851 { 16, Apr, 2013, RCR, "3dmaxima", MINOR, TYPE_BUG_FIX, 5852 "modernize dataset coordinate reporting, using proper signs", 5853 "Thanks to G Pagnoni for reporting the issue." 5854 } , 5855 5856 { 15, Apr, 2013, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 5857 "added RESTING STATE NOTE to help", 5858 NULL 5859 } , 5860 5861 { 15, Apr, 2013, RCR, "3dSurf2Vol", MICRO, TYPE_BUG_FIX, 5862 "fixed crash when a surface was not found (struct init)", 5863 "Thanks to H Yang for noting the problem." 5864 } , 5865 5866 { 9, Apr, 2013, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 5867 "fixed computed fitts for REML case (was from 3dDeconvolve)", 5868 "Thanks to G Pagnoni for noting the problem." 5869 } , 5870 5871 { 5, Apr, 2013, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 5872 "added Help web link to class handouts", 5873 NULL 5874 } , 5875 5876 { 5, Apr, 2013, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 5877 "revert -save_orig_skullstrip to -save_skullstrip", 5878 "This should have no effect on results, except for rename of anat_strip\n" 5879 "to anat_ns. It also gets around a temporary name change from AEA.py." 5880 } , 5881 5882 { 27, Mar, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5883 "added -show_group_labels, -label_prefix_keep/_drop", 5884 "Option -label_prefix_drop can be used to remove bandpass regs for 3dRSFC." 5885 } , 5886 5887 { 8, Mar, 2013, RCR, "3dTcat", MINOR, TYPE_NEW_OPT, 5888 "added -TR and -tpattern options", 5889 NULL 5890 } , 5891 5892 { 7, Mar, 2013, RCR, "file_tool", MINOR, TYPE_ENHANCE, 5893 "handle -prefix and -overwrite for -show_bad_backslash", 5894 "The combination can be used to 'fix' bad files." 5895 } , 5896 5897 { 27, Feb, 2013, RCR, "python-general", MICRO, TYPE_NEW_OPT, 5898 "added Ziad's apsearch global options: -all_opts, -h_find, -h_view", 5899 NULL 5900 } , 5901 5902 { 21, Feb, 2013, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 5903 "small help update to include tshift block in example 5c", 5904 "Thanks to J Gonzalez bringing it up." 5905 } , 5906 5907 { 14, Feb, 2013, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 5908 "handle surface data in -move_preproc_files", 5909 "Thanks to P Molfese for reporting the error." 5910 } , 5911 5912 { 13, Feb, 2013, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 5913 "inform user of subj_dir when writing AP command", 5914 NULL 5915 } , 5916 5917 { 13, Feb, 2013, RCR, "unix_tutorial", MAJOR, TYPE_NEW_PROG, 5918 "added tutorial to CVS tree, with processed files under AFNI_data6", 5919 NULL 5920 } , 5921 5922 { 12, Feb, 2013, RCR, "afni_util.py", MICRO, TYPE_BUG_FIX, 5923 "updated duplicate dataset error message to match older code updates", 5924 "Thanks to HJ Jo for reporting the error." 5925 } , 5926 5927 { 12, Feb, 2013, RCR, "@update.afni.binaries", MICRO, TYPE_BUG_FIX, 5928 "if 'afni -ver' fails from libraries and $status not set, check $package", 5929 NULL 5930 } , 5931 5932 { 11, Feb, 2013, RCR, "file_tool", MICRO, TYPE_ENHANCE, 5933 "help updates", 5934 NULL 5935 } , 5936 5937 { 5, Feb, 2013, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 5938 "updates to the help introduction", 5939 NULL 5940 } , 5941 5942 { 5, Feb, 2013, RCR, "python-general", MICRO, TYPE_BUG_FIX, 5943 "fixed (unused) cols_by_label_list functions", 5944 "Fix by I Schwabacher, who is actually using the function." 5945 } , 5946 5947 { 31, Jan, 2013, RCR, "uber_proc.py", MICRO, TYPE_BUG_FIX, 5948 "fixed blist error that had not been converted to bdict", 5949 "Thanks to Piero C. for reporting the error." 5950 } , 5951 5952 { 30, Jan, 2013, RCR, "python-general", MINOR, TYPE_ENHANCE, 5953 "added less biased correlations and various gcor utility functions", 5954 NULL 5955 } , 5956 5957 { 24, Jan, 2013, RCR, "Dimon", MINOR, TYPE_ENHANCE, 5958 "be able to process a run of AFNI volumes (-file_type AFNI)", 5959 "added for Der-Yow Chen and Cecil Yen" 5960 } , 5961 5962 { 24, Jan, 2013, RCR, "3dinfo", MICRO, TYPE_MODIFY, 5963 "get -orient output via new THD_fill_orient_str_3", 5964 NULL 5965 } , 5966 5967 { 22, Jan, 2013, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 5968 "added -file_type, in prep for reading AFNI/NIfTI images", 5969 NULL 5970 } , 5971 5972 { 18, Jan, 2013, RCR, "@compute_gcor", MINOR, TYPE_NEW_PROG, 5973 "compute GCOR = global correlation of a dataset", 5974 NULL 5975 } , 5976 5977 { 18, Jan, 2013, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 5978 "when jobs=1, only warn for -virtvec if the option was used", 5979 "The result was just a warning which did not affect processing.\n" 5980 "Thanks to J Britton and E Ronkin for reporting the warning." 5981 } , 5982 5983 { 16, Jan, 2013, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 5984 "added option -show_gcor (and _all and _doc)", 5985 "compute GCOR (average correlation) on 1D files" 5986 } , 5987 5988 { 16, Jan, 2013, RCR, "realtime_receiver.py", MINOR, TYPE_NEW_OPT, 5989 "added option -dc_params", 5990 "To go with new scripts AFNI_data6/realtime.demos/demo.2.fback.*." 5991 } , 5992 5993 { 9, Jan, 2013, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 5994 "added option -regress_compute_gcor", 5995 "If errts and EPI mask exist, GCOR is computed by default." 5996 } , 5997 5998 { 7, Jan, 2013, RCR, "3dTstat", MINOR, TYPE_NEW_OPT, 5999 "added option -l2norm, to compute L2 norm", 6000 NULL 6001 } , 6002 6003 { 2, Jan, 2013, RCR, "3dCM", MICRO, TYPE_BUG_FIX, 6004 "in THD_cmass(), if mask is NOT set, clear data value", 6005 "Found with dglen. This is an old bug, ick." 6006 } , 6007 6008 { 31, Dec, 2012, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 6009 "is_in_labels(): search for longest match", 6010 "To fix failure in the case of both label and labelSUFFIX existing." 6011 } , 6012 6013 { 28, Dec, 2012, RCR, "suma-general", MICRO, TYPE_BUG_FIX, 6014 "mri_polyfit() now takes exar paramter, pass NULL", 6015 NULL 6016 } , 6017 6018 { 21, Dec, 2012, RCR, "@update.afni.binaries", MINOR, TYPE_BUG_FIX, 6019 "change check for recur download by looking for known string in script", 6020 "Thanks to S Lowell for reporting the error." 6021 } , 6022 6023 { 20, Dec, 2012, RCR, "uber_subject.py", MINOR, TYPE_BUG_FIX, 6024 "remove -volreg_tlrc_warp in case of no tlrc block", 6025 "Thanks to P Taylor for reporting the error." 6026 } , 6027 6028 { 19, Dec, 2012, RCR, "afni_restproc.py", MINOR, TYPE_GENERAL, 6029 "Update from Rayus for handling .nii files.", 6030 NULL 6031 } , 6032 6033 { 18, Dec, 2012, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 6034 "have THD_subbrick_minmax fall back to THD_slow_minmax_dset if no STAT", 6035 "This is a fix for 3dSkullStrip on NIfTI dsets.\n" 6036 "Thanks to kelvin for reporting the error." 6037 } , 6038 6039 { 5, Dec, 2012, RCR, "serial_helper", MICRO, TYPE_GENERAL, 6040 "added useless string specifier in snprintf to block compier warnings", 6041 "Requested by Y Halchenko." 6042 } , 6043 6044 { 29, Nov, 2012, RCR, "afni-general", MINOR, TYPE_MODIFY, 6045 "add -f to 'tcsh -c' for getting output from commands", 6046 "Thanks to P Molfese for the suggestion to avoid .cshrc text output." 6047 } , 6048 6049 { 26, Nov, 2012, RCR, "align_epi_anat.py", MINOR, TYPE_NEW_OPT, 6050 "added -save_script option", 6051 "added script history in afni_com class" 6052 } , 6053 6054 { 15, Nov, 2012, RCR, "3dTqual", MINOR, TYPE_NEW_OPT, 6055 "added -mask option", 6056 "Requested by evangelou." 6057 } , 6058 6059 { 14, Nov, 2012, RCR, "make_random_timing.py", MINOR, TYPE_BUG_FIX, 6060 "fixed check for random space in -max_consec case", 6061 "Thanks to Kristina for reporting the error." 6062 } , 6063 6064 { 13, Nov, 2012, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 6065 "fixed fopen_maybe to check for .1D suffix on file streams", 6066 "Suffix might get added by EDIT_dset_items.\n" 6067 "Thanks to I Schwabacher for reporting the error." 6068 } , 6069 6070 { 23, OCT, 2012, RCR, "to3d", MINOR, TYPE_BUG_FIX, 6071 "forgot to leave show_size_n_offset set", 6072 "Thanks to J Jarcho for reporting the to3d failure." 6073 } , 6074 6075 { 19, OCT, 2012, RCR, "file_tool", MINOR, TYPE_ENHANCE, 6076 "added test for BOM bytes (byte order mark)", 6077 NULL 6078 } , 6079 6080 { 18, OCT, 2012, RCR, "file_tool", MINOR, TYPE_ENHANCE, 6081 "added convenience option -test", 6082 NULL 6083 } , 6084 6085 { 18, OCT, 2012, RCR, "uber_ttest.py", MINOR, TYPE_BUG_FIX, 6086 "small updates to correspond with library changes", 6087 NULL 6088 } , 6089 6090 { 17, OCT, 2012, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 6091 "removed unneeded -set_tr from 1d_tool.py -censor_motion", 6092 NULL 6093 } , 6094 6095 { 17, OCT, 2012, RCR, "dicom_hdr", MINOR, TYPE_NEW_OPT, 6096 "added -no_length option, which helps when running diffs on output", 6097 NULL 6098 } , 6099 6100 { 16, OCT, 2012, RCR, "uber_subject.py", MINOR, TYPE_NEW_OPT, 6101 "added analysis type and processing block list", 6102 NULL 6103 } , 6104 6105 { 12, OCT, 2012, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 6106 "included tshift block in example #9 - resting state analysis", 6107 "Thanks to D Drake for reminding me to add it." 6108 } , 6109 6110 { 12, OCT, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6111 "added byte-swapping for complex numbers in thd_niml.c", 6112 NULL 6113 } , 6114 6115 { 12, OCT, 2012, RCR, "@RetinoProc", MICRO, TYPE_BUG_FIX, 6116 "set AEA_opt in quotes, as it might be a list", 6117 NULL 6118 } , 6119 6120 { 5, OCT, 2012, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 6121 "added option -quick_censor_count", 6122 NULL 6123 } , 6124 6125 { 5, OCT, 2012, RCR, "dicom_hinfo", MINOR, TYPE_NEW_OPT, 6126 "added option -no_name", 6127 NULL 6128 } , 6129 6130 { 3, OCT, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6131 "dashed parameters are now illegal for many options in many python programs", 6132 "Affects programs:\n" 6133 " 1d_tool.py, afni_proc.py, gen_group_command.py, make_random_timing.py,\n" 6134 " make_stim_times.py, option_list.py, timing_tool.py" 6135 } , 6136 6137 { 2, OCT, 2012, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 6138 "added stim_type column to stim table", 6139 "This corresponds to the afni_proc.py option -regress_stim_types." 6140 } , 6141 6142 { 2, OCT, 2012, RCR, "model_conv_diffgamma", MICRO, TYPE_GENERAL, 6143 "small help update", 6144 NULL 6145 } , 6146 6147 { 1, OCT, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6148 "added 'file' to list of -stim_types parameters", 6149 "The 'file' type would imply -stim_file in 3dDeconvolve, not timing." 6150 } , 6151 6152 { 26, SEP, 2012, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_OPT, 6153 "added -apsearch; verify download for recursive step", 6154 NULL 6155 } , 6156 6157 { 26, SEP, 2012, RCR, "nifti_tool", MINOR, TYPE_BUG_FIX, 6158 "changed ana originator field from char to short", 6159 NULL 6160 } , 6161 6162 { 25, SEP, 2012, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 6163 "use errts_REML to compute blur if 3dD_stop; apply compute_fitts if no reml", 6164 "Thanks to P Molfese for reporting the problem." 6165 } , 6166 6167 { 21, SEP, 2012, RCR, "3dNLfim", MICRO, TYPE_GENERAL, 6168 "added ConvDiffGam to help", 6169 NULL 6170 } , 6171 6172 { 20, SEP, 2012, RCR, "3dClustSim", MICRO, TYPE_GENERAL, 6173 "added a note to the help about computing blur estimates", 6174 "Requested by J Weisberg." 6175 } , 6176 6177 { 20, SEP, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6178 "added some projection function to python libraries", 6179 NULL 6180 } , 6181 6182 { 13, SEP, 2012, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 6183 "download and run the current version on the web site", 6184 "Good idea, Bob." 6185 } , 6186 6187 { 13, SEP, 2012, RCR, "afni_util", MINOR, TYPE_ENHANCE, 6188 "can call list functions via -listfunc (to avoid input formatting)", 6189 "Also, use -join after the LISTFUNC to remove list format on output, e.g.\n" 6190 "\ncd AFNI_data6\n" 6191 "afni_util.py -listfunc list_minus_glob_form -join group_results/OLSQ*.HEAD" 6192 } , 6193 6194 { 6, SEP, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6195 "if varying facs/types on NIfTI write, write floats instead of failing", 6196 NULL 6197 } , 6198 6199 { 6, SEP, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 6200 "print missing xmat error w/out debug, as it is fatal", 6201 NULL 6202 } , 6203 6204 { 6, SEP, 2012, RCR, "afni-general", MINOR, TYPE_NEW_OPT, 6205 "apply global opt -pad_to_node when going through AFNI format in thd_niml.c", 6206 NULL 6207 } , 6208 6209 { 4, SEP, 2012, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6210 "added option -regress_ROI", 6211 "This allows for tissue-based regression, with ROI averages from any of:\n" 6212 " brain (from full_mask), GM, WM and CSF (from Classes_resam)\n" 6213 "The 'mask' block is required for all ROIs, and option -mask_segment_anat\n" 6214 "is required for the latter 3." 6215 } , 6216 6217 { 4, SEP, 2012, RCR, "gen_group_command.py", MICRO, TYPE_BUG_FIX, 6218 "fixed error message in case of different group sizes", 6219 "Error pointed out by Priyank." 6220 } , 6221 6222 { 31, AUG, 2012, RCR, "3dTstat", MINOR, TYPE_NEW_OPT, 6223 "added option -signed_absmax", 6224 "Requested by P Hamilton." 6225 } , 6226 6227 { 30, AUG, 2012, RCR, "1d_tool.py", MICRO, TYPE_MODIFY, 6228 "display -show_mmms output to 4 places", 6229 NULL 6230 } , 6231 6232 { 24, AUG, 2012, RCR, "column_cat", MAJOR, TYPE_NEW_PROG, 6233 "like 'cat', except horizontally (see recent Unix command, 'paste')", 6234 NULL 6235 } , 6236 6237 { 23, AUG, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_NEW_OPT, 6238 "can pass -censor_dset", 6239 NULL 6240 } , 6241 6242 { 21, AUG, 2012, RCR, "slow_surf_clustsim.py", MICRO, TYPE_NEW_OPT, 6243 "added 'sigma' uvar, for passing to SurfSmooth", 6244 NULL 6245 } , 6246 6247 { 17, AUG, 2012, RCR, "3dGroupInCorr", MICRO, TYPE_BUG_FIX, 6248 "pass 'batch mode' var to SUMA_init_GISET_setup to preserve dset", 6249 NULL 6250 } , 6251 6252 { 16, AUG, 2012, RCR, "gen_group_command.py", MICRO, TYPE_MODIFY, 6253 "show datasets names when a 'labels not unique' error occurs", 6254 NULL 6255 } , 6256 6257 { 14, AUG, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6258 "match default class order for 3dSeg; copy labeltable into resampled dset", 6259 NULL 6260 } , 6261 6262 { 10, AUG, 2012, RCR, "afni_restproc.py", MINOR, TYPE_GENERAL, 6263 "Updates from Rayus.", 6264 "Fixed bugs with -outcensor and -snr.\n" 6265 "Added -bpassregs and -keepuncensored.\n" 6266 "Use variable detrending for -tsnr." 6267 } , 6268 6269 { 9, AUG, 2012, RCR, "afni_general", MICRO, TYPE_BUG_FIX, 6270 "definition after ENTRY in mri_genalign_util.c", 6271 NULL 6272 } , 6273 6274 { 8, AUG, 2012, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 6275 "added -use_slice_loc; fixed app of use_last_elem in mri_read_dicom", 6276 "g_info.use_last_elem has usurped the lone global" 6277 } , 6278 6279 { 8, AUG, 2012, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 6280 "do not update tlrc anat with strip if passed in", 6281 NULL 6282 } , 6283 6284 { 8, AUG, 2012, RCR, "slow_surf_clustsim.py", MICRO, TYPE_BUG_FIX, 6285 "currently need to pass -sv even for -on_surface; get rid of this later", 6286 NULL 6287 } , 6288 6289 { 31, JUL, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6290 "have -mask_segment_anat default to no (libgsl is not quite so common)", 6291 NULL 6292 } , 6293 6294 { 31, JUL, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6295 "speed up reading NIfTI files with long histories (THD_dblkatr_from_niml)", 6296 "Thanks to J Gonzalez for reporting the problem." 6297 } , 6298 6299 { 31, JUL, 2012, RCR, "3dresample", MINOR, TYPE_BUG_FIX, 6300 "update IJK_TO_DICOM and _REAL at end of resample library function", 6301 "Thanks to I Schwabacher for reporting the IJK_TO_DICOM discrepancy." 6302 } , 6303 6304 { 30, JUL, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6305 "if surface analysis, create run_suma script", 6306 NULL 6307 } , 6308 6309 { 30, JUL, 2012, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 6310 "added -show_mmms", 6311 "Display min, mean, max, stdev of each column." 6312 } , 6313 6314 { 26, JUL, 2012, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6315 "added -mask_segment_anat and -mask_rm_segsy", 6316 "If anat is stripped, create segmented anat unless user says not to." 6317 } , 6318 6319 { 26, JUL, 2012, RCR, "3dttest++", MINOR, TYPE_BUG_FIX, 6320 "K text columns (after label) would result in K lost float columns", 6321 "Thanks to Phoebe of Harvard for reporting the problem." 6322 } , 6323 6324 { 26, JUL, 2012, RCR, "realtime_receiver.py", MINOR, TYPE_NEW_OPT, 6325 "added -show_comm_times option to show communication times", 6326 "Added for J Evans (and to get it off an ancient todo list)." 6327 } , 6328 6329 { 23, JUL, 2012, RCR, "afni-general", MICRO, TYPE_ENHANCE, 6330 "allow programs to read auto-tcat datasets using filelist:DSETS.txt", 6331 "If DSETS.txt contains a list of datasets, they will be read in using\n" 6332 "THD_open_tcat(), as if they were listed separated by spaces.\n\n" 6333 "Added for C Connolly." 6334 } , 6335 6336 { 20, JUL, 2012, RCR, "apsearch", MICRO, TYPE_MODIFY, 6337 "exclude README.* from program list", 6338 "Executable README files can be troublesome..." 6339 } , 6340 6341 { 17, JUL, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 6342 "added checks for volreg and uncensored X-mat; get view from volreg", 6343 NULL 6344 } , 6345 6346 { 17, JUL, 2012, RCR, "slow_surf_clustsim.py", MICRO, TYPE_MODIFY, 6347 "removed -Niter opt from SurfSmooth (let it decide)", 6348 NULL 6349 } , 6350 6351 { 11, JUL, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6352 "fill gaps and holes in anatomical masks", 6353 "(now requires AFNI from 7 May, 2012)" 6354 } , 6355 6356 { 10, JUL, 2012, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 6357 "let the user know whether 3dClustSim will be run", 6358 NULL 6359 } , 6360 6361 { 9, JUL, 2012, RCR, "@auto_tlrc", MICRO, TYPE_MODIFY, 6362 "escape (unalias) every 'rm' command", 6363 NULL 6364 } , 6365 6366 { 9, JUL, 2012, RCR, "align_epi_anat.py", MICRO, TYPE_MODIFY, 6367 "escape (unalias) every 'rm' command", 6368 NULL 6369 } , 6370 6371 { 29, JUN, 2012, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 6372 "moved ptaylor_install dependency from 'vastness' to 'install'", 6373 NULL 6374 } , 6375 6376 { 29, JUN, 2012, RCR, "prompt_user", MICRO, TYPE_NEW_OPT, 6377 "if MESSAGE is '-', read from stdin", 6378 NULL 6379 } , 6380 6381 { 29, JUN, 2012, RCR, "@Install_RSFMRI_Motion_Group_Demo", MINOR, TYPE_NEW_PROG, 6382 "program is for installing demo of RSFMR on big and small motion groups", 6383 NULL 6384 } , 6385 6386 { 28, JUN, 2012, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 6387 "fixed help error regarding IM", 6388 "Thanks to I Blair for reporting it." 6389 } , 6390 6391 { 27, JUN, 2012, RCR, "3dTstat", MICRO, TYPE_NEW_OPT, 6392 "added -nzmedian, requested on message board", 6393 NULL 6394 } , 6395 6396 { 25, JUN, 2012, RCR, "gen_group_command.py", MICRO, TYPE_ENHANCE, 6397 "added help for -factors and 3dANOVA3 -type 4 examples", 6398 NULL 6399 } , 6400 6401 { 25, JUN, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 6402 "fixed uninitialized cpad1,2 in the case of no censoring", 6403 NULL 6404 } , 6405 6406 { 22, JUN, 2012, RCR, "gen_group_command.py", MINOR, TYPE_NEW_OPT, 6407 "added commands 3dANOVA2 and 3dANOVA3; added option -factors", 6408 "Need to add help for -factors (i.e. for 3dANOVA3 -type 4)." 6409 } , 6410 6411 { 20, JUN, 2012, RCR, "plug_realtime", MICRO, TYPE_BUG_FIX, 6412 "comment out plot_ts_setthik() type calls for now", 6413 "When registering, finalize_dset() will result in white image window.\n" 6414 "Thanks to V Roopchansingh for reporting the problem." 6415 } , 6416 6417 { 15, JUN, 2012, RCR, "GIFTI", MINOR, TYPE_MODIFY, 6418 "make num_dim violation a warning, because of mris_convert", 6419 NULL 6420 } , 6421 6422 { 15, JUN, 2012, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6423 "added -regress_censor_extern", 6424 NULL 6425 } , 6426 6427 { 14, JUN, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 6428 "use afni -com instead of plugout_drive (for case of multiple users)", 6429 "Thanks to V Razdan and N Adleman for reporting the issue." 6430 } , 6431 6432 { 6, JUN, 2012, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 6433 "look for input of EPI datasets in standard space and NIfTI format", 6434 NULL 6435 } , 6436 6437 { 5, JUN, 2012, RCR, "3dmask_tool", MICRO, TYPE_BUG_FIX, 6438 "need to explicitly set DSET_BRICK_TYPE() on some systems", 6439 NULL 6440 } , 6441 6442 { 5, JUN, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6443 "warn users if married types and files do not seem to match", 6444 NULL 6445 } , 6446 6447 { 3, JUN, 2012, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 6448 "for resting state analysis, suggest -regress_censor_motion 0.2", 6449 "Suggest a more strict limit for resting state than for task analysis." 6450 } , 6451 6452 { 3, JUN, 2012, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 6453 "for variable updates: actually show list if it is short enough", 6454 NULL 6455 } , 6456 6457 { 25, MAY, 2012, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 6458 "display modified options and subject defaults", 6459 NULL 6460 } , 6461 6462 { 22, MAY, 2012, RCR, "uber_subject.py", MINOR, TYPE_NEW_OPT, 6463 "added regress_bandpass and regress_mot_deriv (probably for resting state)", 6464 NULL 6465 } , 6466 6467 { 21, MAY, 2012, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6468 "added the long-desired-but-not-so-needed -regress_stim_types option", 6469 "This allows users to specify -stim_times/_AM1/_AM2/_IM." 6470 } , 6471 6472 { 19, MAY, 2012, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 6473 "added help examples for resting state analysis", 6474 NULL 6475 } , 6476 6477 { 19, MAY, 2012, RCR, "afni-general", MICRO, TYPE_ENHANCE, 6478 "allow for auto-tcat of 1D inputs that are separated by spaces", 6479 "For E Demir to use in 3dDeconovolve." 6480 } , 6481 6482 { 16, MAY, 2012, RCR, "@GetAfniOrient", MICRO, TYPE_MODIFY, 6483 "suppress 3dinfo version text", 6484 NULL 6485 } , 6486 6487 { 16, MAY, 2012, RCR, "@auto_tlrc", MICRO, TYPE_MODIFY, 6488 "do not ask for user input, even if centers are off by 80+ mm", 6489 NULL 6490 } , 6491 6492 { 11, MAY, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6493 "also output average censored per-TR motion", 6494 NULL 6495 } , 6496 6497 { 10, MAY, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6498 "allow processing of more than 99 runs", 6499 NULL 6500 } , 6501 6502 { 10, MAY, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6503 "allow for a wider range of file names", 6504 "- handle case of more than 99 runs\n" 6505 "- look for files of the form *_rall.1D, as well as *.rall.1D" 6506 } , 6507 6508 { 7, MAY, 2012, RCR, "3dmask_tool", MINOR, TYPE_ENHANCE, 6509 "replaced THD_mask_erode with new THD_mask_erode_sym", 6510 "This change should make dilate and erosion operations symmetric." 6511 } , 6512 6513 { 7, MAY, 2012, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 6514 "added weighted_enorm method for -collapse_cols; added -weight_vec", 6515 NULL 6516 } , 6517 6518 { 4, MAY, 2012, RCR, "afni_restproc.py", MINOR, TYPE_BUG_FIX, 6519 "submitting updates from Rayus", 6520 "Updates are in changelog." 6521 } , 6522 6523 { 3, MAY, 2012, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 6524 "added -backward_diff and -forward_diff", 6525 "Note, -backward_diff is the same as -derivative." 6526 } , 6527 6528 { 2, MAY, 2012, RCR, "afni-general", MICRO, TYPE_ENHANCE, 6529 "added AFNI_PATH_SPACES_OK, for input of datasets with spaces in path", 6530 "Added for V Roopchansingh." 6531 } , 6532 6533 { 1, MAY, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6534 "added -prefix option; added censor coloring to 1dplot commands", 6535 NULL 6536 } , 6537 6538 { 1, MAY, 2012, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 6539 "added -looks_like_AM", 6540 NULL 6541 } , 6542 6543 { 1, MAY, 2012, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 6544 "allowed -ordered_stimuli and -max_consec, together", 6545 "Requested by Liat." 6546 } , 6547 6548 { 30, APR, 2012, RCR, "afni_restproc.py", MAJOR, TYPE_NEW_PROG, 6549 "this program is by Rayus Kuplicki, please contact him for information", 6550 NULL 6551 } , 6552 6553 { 27, APR, 2012, RCR, "3dmask_tool", MAJOR, TYPE_NEW_PROG, 6554 "a program to manipulate mask datasets", 6555 NULL 6556 } , 6557 6558 { 24, APR, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6559 "if surface data with generic prefix, append surf-type suffix", 6560 "Done to fix ANOVA commands on surface.\n" 6561 "Thanks to R Ray for bringing this up." 6562 } , 6563 6564 { 17, APR, 2012, RCR, "afni-general", MINOR, TYPE_ENHANCE, 6565 "added atlas/ROI label use with <> range selectors (MCW_get_angle_range)", 6566 NULL 6567 } , 6568 6569 { 16, APR, 2012, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 6570 "added -regress_bandpass, for bandpass filtering via regression", 6571 NULL 6572 } , 6573 6574 { 13, APR, 2012, RCR, "@radial_correlate.py", MICRO, TYPE_ENHANCE, 6575 "accept +tlrc datasets", 6576 NULL 6577 } , 6578 6579 { 12, APR, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 6580 "backport to python 2.2", 6581 NULL 6582 } , 6583 6584 { 12, APR, 2012, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 6585 "backport to python 2.2", 6586 "For files that should work on 2.2, avoid sum() and enumerate().\n" 6587 "Thanks to L Broster for reporting problems on python 2.2." 6588 } , 6589 6590 { 8, APR, 2012, RCR, "make_random_timing.py", MINOR, TYPE_ENHANCE, 6591 "-ordered_stimuli now takes labels", 6592 NULL 6593 } , 6594 6595 { 4, APR, 2012, RCR, "afni-general", MINOR, TYPE_MODIFY, 6596 "if prefix shows STORAGE_UNDEFINED, use BRIK only if not potential surface", 6597 NULL 6598 } , 6599 6600 { 3, APR, 2012, RCR, "plug_realtime", MICRO, TYPE_MODIFY, 6601 "always print the name of the mask dataset in use (via GUI or env)", 6602 NULL 6603 } , 6604 6605 { 30, MAR, 2012, RCR, "plug_realtime", MICRO, TYPE_MODIFY, 6606 "let user know when AFNI_REALTIME_Mask_Dset is applied", 6607 NULL 6608 } , 6609 6610 { 30, MAR, 2012, RCR, "@auto_tlrc", MICRO, TYPE_NEW_OPT, 6611 "added option -inweight\n", 6612 "Added for S Horovitz and S Tinaz." 6613 } , 6614 6615 { 22, MAR, 2012, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 6616 "apply AFNI_REALTIME_SHOW_TIMES in non-RT feedback case", 6617 NULL 6618 } , 6619 6620 { 22, MAR, 2012, RCR, "Dimon", MICRO, TYPE_ENHANCE, 6621 "if RT comm fails with afni, show iochan_error_string()", 6622 "It occasionally fails at TR=0.125 s." 6623 } , 6624 6625 { 21, MAR, 2012, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 6626 "use run_lengths for TR list; removed path from external motion file", 6627 NULL 6628 } , 6629 6630 { 21, MAR, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 6631 "look for more motion files; minor changes to output format", 6632 NULL 6633 } , 6634 6635 { 21, MAR, 2012, RCR, "3dcalc", MICRO, TYPE_ENHANCE, 6636 "added -help description to -help output", 6637 "To get apsearch to enable <tab> completion of -help option." 6638 } , 6639 6640 { 15, MAR, 2012, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 6641 "added AFNI_REALTIME_Mask_Dset for per-run control over Mask", 6642 "Also added some missing vars to README.environment.\n" 6643 "Done for J Evans." 6644 } , 6645 6646 { 14, MAR, 2012, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 6647 "added -num_chan and -max_quiet_trs; default sleep = 1.1*TR, max of 2", 6648 "Added for J Evans and V Roopchansingh." 6649 } , 6650 6651 { 14, MAR, 2012, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 6652 "test for global timing before local, as it looks like bad local", 6653 "Thanks to P Pallett for reporting the problem." 6654 } , 6655 6656 { 13, MAR, 2012, RCR, "lib_qt_gui.py", MICRO, TYPE_MODIFY, 6657 "has main, so added trivial -help option", 6658 NULL 6659 } , 6660 6661 { 12, MAR, 2012, RCR, "@SUMA_AlignToExperiment", MICRO, TYPE_NEW_OPT, 6662 "added -overwrite_resp, so that processing does not have to stop and wait", 6663 "Also, used 'find' grab *.nii, to fix the failure reported by R Ray.\n" 6664 "Forgot to put this in with the afni_proc.py change..." 6665 } , 6666 6667 { 9, MAR, 2012, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 6668 "added $hemi to rm.mean dset during scaling; added -overwrite_resp to SATE", 6669 "Surface analysis would fail on 2nd hemi, as rm.mean dset would exist." 6670 "Also, added new '-overwrite_resp S' to @SUMA_AlignToExperiement command." 6671 } , 6672 6673 { 7, MAR, 2012, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 6674 "existing package and install dir no longer required for -defaults", 6675 NULL 6676 } , 6677 6678 { 7, MAR, 2012, RCR, "GIFTI", MICRO, TYPE_BUG_FIX, 6679 "fixed sizeof in memset of gim (noted by B Cox)", 6680 NULL 6681 } , 6682 6683 { 6, MAR, 2012, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 6684 "move nokia help to -help_install_nokia (since it is not recommended)", 6685 NULL 6686 } , 6687 6688 { 5, MAR, 2012, RCR, "apsearch", MICRO, TYPE_MODIFY, 6689 "do not set shell variables", 6690 NULL 6691 } , 6692 6693 { 5, MAR, 2012, RCR, "uber_proc.py", MICRO, TYPE_MODIFY, 6694 "trivially apply -help option, for apsearch", 6695 NULL 6696 } , 6697 6698 { 5, MAR, 2012, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 6699 "EDIT_empty: only propagate writable storage_modes", 6700 "Added is_writable_storage_mode and DSET_STORAGE_MODE.\n" 6701 "Thanks to Eli for reporting the problem." 6702 } , 6703 6704 { 2, MAR, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6705 "fixed $runs in multi-run ricor", 6706 "Thanks to I Mukai for reporting the problem." 6707 } , 6708 6709 { 27, FEB, 2012, RCR, "@update.afni.binaries", MINOR, TYPE_ENHANCE, 6710 "made a little more intelligent, e.g. make one backup by default", 6711 "Note: can run this without any existing AFNI binaries, e.g.\n" 6712 " @update.afni.binaries -bindir ~/abin -package linux_openmotif" 6713 } , 6714 6715 { 24, FEB, 2012, RCR, "1d_tool.py", MINOR, TYPE_MODIFY, 6716 "added -moderate_mask, fixed -extreme_mask help", 6717 "Thanks to R Kuplicki for reporting the help inconsistency." 6718 } , 6719 6720 { 22, FEB, 2012, RCR, "afni-general", MINOR, TYPE_MODIFY, 6721 "moved GLOBAL_browser def from afni.h to thd_ttatlas_query.c", 6722 "- declared in TTQ.h\n" 6723 "- deleted #include thd_atlas.h from most .c files\n" 6724 "- #include thd_atlas.h in mrilib.h" 6725 } , 6726 6727 { 22, FEB, 2012, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 6728 "added -randomize_trs and -seed", 6729 "Affected 1d_tool.py, afni_util.py, lib_afni1D.py and lib_textdata.py." 6730 } , 6731 6732 { 21, FEB, 2012, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 6733 "if destination directory is not writable, let the user know", 6734 NULL 6735 } , 6736 6737 { 16, FEB, 2012, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 6738 "more quick termination updates", 6739 "- added -max_images\n" 6740 "- do not init vol search state to 2, would limit volumes to 40\n" 6741 "- include fl_start in no_wait test\n" 6742 "- look for new vol worth of images, but no volume match" 6743 } , 6744 6745 { 14, FEB, 2012, RCR, "Dimon", MINOR, TYPE_MODIFY, 6746 "if -no_wait, terminate on volume_match failure", 6747 "For F Ye." 6748 } , 6749 6750 { 14, FEB, 2012, RCR, "uber_ttest.py", MINOR, TYPE_ENHANCE, 6751 "release version 1.0: help, copy tables, scripts imply -no_gui", 6752 NULL 6753 } , 6754 6755 { 10, FEB, 2012, RCR, "uber_ttest.py", MINOR, TYPE_ENHANCE, 6756 "added 'paired' toggle box to GUI", 6757 NULL 6758 } , 6759 6760 { 10, FEB, 2012, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 6761 "added -check_results_dir for Z Saad", 6762 "Also, changed -tcat_outlier_warn_limit to -tcat_preSS_warn_limit." 6763 } , 6764 6765 { 10, FEB, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 6766 "make tcat files optional; apply prefix to 'basic' commands in driver", 6767 NULL 6768 } , 6769 6770 { 10, FEB, 2012, RCR, "slow_surf_clustsim.py", MICRO, TYPE_MODIFY, 6771 "tiny help update, as enforced by H Jo", 6772 NULL 6773 } , 6774 6775 { 6, FEB, 2012, RCR, "Dimon", MINOR, TYPE_ENHANCE, 6776 "added -no_wait option: never wait for new data", 6777 "Also, suppress new glob warnings.\n" 6778 "Done for F Ye and others." 6779 } , 6780 6781 { 6, FEB, 2012, RCR, "to3d", MICRO, TYPE_MODIFY, 6782 "tiny help update, as enforced by D Glen", 6783 NULL 6784 } , 6785 6786 { 6, FEB, 2012, RCR, "3dsvm", MICRO, TYPE_MODIFY, 6787 "applied Makefile.INCLUDE updates for J Lisinski and S LaConte", 6788 NULL 6789 } , 6790 6791 { 3, FEB, 2012, RCR, "align_epi_anat.py", MICRO, TYPE_BUG_FIX, 6792 "updated @AddEdge command to match change to afni_base:shell_com", 6793 "Done with D Glen." 6794 } , 6795 6796 { 2, FEB, 2012, RCR, "uber_ttest.py", MINOR, TYPE_ENHANCE, 6797 "added basic 3dMEMA capabilities", 6798 "This affected afni_util.py, ask_me.py, gui_uber_ttest.py, lib_qt_gui.py\n" 6799 " lib_subjects.py, lib_uber_ttest.py, uber_subject.py, uber_ttest.py." 6800 } , 6801 6802 { 1, FEB, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_ENHANCE, 6803 "check for pre-steady state outlier warnings", 6804 NULL 6805 } , 6806 6807 { 1, FEB, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6808 "check for pre-steady state outlier counts", 6809 "Added option -tcat_outlier_warn_limit." 6810 } , 6811 6812 { 31, JAN, 2012, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6813 "look for aligned anat _al_junk/keep", 6814 NULL 6815 } , 6816 6817 { 31, JAN, 2012, RCR, "to3d", MINOR, TYPE_BUG_FIX, 6818 "also update check for '### ASCCONV BEGIN' in to3d...", 6819 "Problem noted by J Lewis." 6820 } , 6821 6822 { 31, JAN, 2012, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6823 "added -regress_apply_ricor", 6824 NULL 6825 } , 6826 6827 { 30, JAN, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6828 "ricor block: no longer apply in later 3dDeconvolve", 6829 "The regressors for slice #0 from the ricor block were being applied in\n" 6830 "the final regression (to remove motion) for consistency in degrees of\n" 6831 "freedom. But we might rather not do that, particularly since DOF are\n" 6832 "not important when proceeding with just correlation coefficients." 6833 } , 6834 6835 { 30, JAN, 2012, RCR, "uber_ttest.py", MICRO, TYPE_MODIFY, 6836 "all python files use '/usr/bin/env python' instead of '/usr/bin/python'", 6837 "modified afni_base.py, gui_uber_align_test.py, gui_uber_subj.py,\n" 6838 " uber_skel.py, @DoPerRoi.py, gui_uber_skel.py, gui_uber_ttest.py,\n" 6839 " uber_ttest.py" 6840 } , 6841 6842 { 28, JAN, 2012, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 6843 "look for TSNR* in case of surf analysis", 6844 NULL 6845 } , 6846 6847 { 28, JAN, 2012, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6848 "updates for surf analysis of subject FT under AFNI_data6", 6849 " - added -atlas_followers to @SUMA_AlignToExperiment\n" 6850 " - if surf analysis: no scaling mask (e.g. extents)\n" 6851 " - updated help example #8 for surf analysis of AFNI_data6 subject FT" 6852 } , 6853 6854 { 27, JAN, 2012, RCR, "to3d", MINOR, TYPE_BUG_FIX, 6855 "fix inf loop if some sSliceArray entries not set", 6856 "Also, now there might be junk between ASCCONV BEGIN and ###, grrrrr...\n" 6857 "Problem noted by J Lewis." 6858 } , 6859 6860 { 25, JAN, 2012, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 6861 "back out overzealous -quit changes for now", 6862 NULL 6863 } , 6864 6865 { 20, JAN, 2012, RCR, "to3d", MINOR, TYPE_MODIFY, 6866 "mri_read_dicom: if there is no VALID vrCode, skip explicitVR", 6867 "Done for Chad N." 6868 } , 6869 6870 { 19, JAN, 2012, RCR, "Dimon", MINOR, TYPE_MODIFY, 6871 "made -quit more aggressive", 6872 NULL 6873 } , 6874 6875 { 18, JAN, 2012, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6876 "force anat variable (and children) to be in AFNI format after 3dcopy", 6877 "Appropriate, and for compatibility with an afni_name.pv change." 6878 } , 6879 6880 { 17, JAN, 2012, RCR, "Dimon", MINOR, TYPE_MODIFY, 6881 "-gert_create_dataset now implies -GERT_Reco and -quit", 6882 "For Ziad and Daniel." 6883 } , 6884 6885 { 12, JAN, 2012, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 6886 "fixed ricor block 3dcalc loop for varying run lengths", 6887 NULL 6888 } , 6889 6890 { 11, JAN, 2012, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 6891 "dx and dy were reversed in mri_read_dicom.c", 6892 "Thanks to P Kaskan and F Ye for bringing this up." 6893 } , 6894 6895 { 28, NOV, 2011, RCR, "1dnorm", MICRO, TYPE_BUG_FIX, 6896 "re-enabled use of '-' for stdin/stdout", 6897 "Requested by R Birn." 6898 } , 6899 6900 { 22, NOV, 2011, RCR, "uber_subject.py", MINOR, TYPE_NEW_OPT, 6901 "allow for passing variables directly, not via -svar", 6902 NULL 6903 } , 6904 6905 { 21, NOV, 2011, RCR, "quick.alpha.vals.py", MINOR, TYPE_NEW_PROG, 6906 "a very simple program to tabulate the output from slow_surf_clustsim.py", 6907 "This ought to be improved, but at least it is now distributed..." 6908 } , 6909 6910 { 21, NOV, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 6911 "small update to help text", 6912 NULL 6913 } , 6914 6915 { 21, NOV, 2011, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 6916 "fixed -ynames in plot of motion/outliers", 6917 NULL 6918 } , 6919 6920 { 17, NOV, 2011, RCR, "@ROI_Corr_Mat", MICRO, TYPE_BUG_FIX, 6921 "fix complaint about unknown options for non-macs", 6922 NULL 6923 } , 6924 6925 { 17, NOV, 2011, RCR, "afni", MINOR, TYPE_BUG_FIX, 6926 "if dset+orig is anat/func and dset+tlrc is func/anat, 'BAD dataset', man", 6927 "Altered logic in thd_initsess.c (done with dglen)." 6928 } , 6929 6930 { 17, NOV, 2011, RCR, "3drefit", MICRO, TYPE_BUG_FIX, 6931 "changing 'type' should have an effect even if not a bucket", 6932 "Done with dglen." 6933 } , 6934 6935 { 9, NOV, 2011, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 6936 "-surf_blur_fwhm is no longer valid, please use -blur_size", 6937 NULL 6938 } , 6939 6940 { 8, NOV, 2011, RCR, "adwarp", MICRO, TYPE_ENHANCE, 6941 "added a help example for writing anat+tlrc.BRIK", 6942 NULL 6943 } , 6944 6945 { 7, NOV, 2011, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 6946 "added -blur_to_fwhm and -blur_opts_B2FW", 6947 "Added for E Nelson and J Jarcho." 6948 } , 6949 6950 { 4, NOV, 2011, RCR, "3dSurf2Vol", MINOR, TYPE_ENHANCE, 6951 "added 'mode' mapping function", 6952 "Requested by R Mruczek. Also done for Z Puckett." 6953 } , 6954 6955 { 3, NOV, 2011, RCR, "@2dwarper.Allin", MINOR, TYPE_NEW_OPT, 6956 "added -prefix option; allow for 3dAllin failures; copy time info", 6957 "Updates by N Mei and A Messinger." 6958 } , 6959 6960 { 2, NOV, 2011, RCR, "Dimon", MINOR, TYPE_ENHANCE, 6961 "allow -save_file_list to apply even with -infile_list", 6962 NULL 6963 } , 6964 6965 { 2, NOV, 2011, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 6966 "if using TENT, run 'timing_tool.py -warn_tr_stats'", 6967 "Warnings are also saved in out.TENT_warn.txt." 6968 } , 6969 6970 { 2, NOV, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6971 "added out.TENT_warn.txt to warning file review", 6972 NULL 6973 } , 6974 6975 { 31, OCT, 2011, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 6976 "added -show_tr_stats and -warn_tr_stats options", 6977 NULL 6978 } , 6979 6980 { 25, OCT, 2011, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 6981 "process married files with current operations", 6982 "1. AfniMarriedTiming inherits from AfniData (instead of local copies)\n" 6983 "2. add all AfniTiming methods to AfniMarriedTiming (as married timing)\n" 6984 "3. rename AfniMarriedTiming back to AfniTiming (but now married)" 6985 } , 6986 6987 { 25, OCT, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 6988 "look for more file name variants, including with '_' separators", 6989 "Added for J Weisberg." 6990 } , 6991 6992 { 20, OCT, 2011, RCR, "afni_general", MINOR, TYPE_MODIFY, 6993 "changed most resampling programs to deoblique inputs upon read", 6994 "THD_open*_dataset() was followed by THD_make_cardinal().\n" 6995 "modified: 3dresample, 3dfractionize, 3drotate, adwarp, 3dLRflip\n" 6996 " 3dZeropad, 3dZcat, 3dAutobox\n" 6997 "not (yet) modified: 3dWarp(Drive), 3dAllineate" 6998 } , 6999 7000 { 19, OCT, 2011, RCR, "@2dwarper.Allin", MICRO, TYPE_NEW_OPT, 7001 "added a -mask option", 7002 "Added for A Messinger." 7003 } , 7004 7005 { 19, OCT, 2011, RCR, "GIFTI", MINOR, TYPE_ENHANCE, 7006 "can read/write ascii COMPLEX64, COMPLEX128, RGB24", 7007 "Requested by H Breman, J Mulders and N Schmansky." 7008 } , 7009 7010 { 18, OCT, 2011, RCR, "uber_subject.py", MINOR, TYPE_NEW_OPT, 7011 "added blur size control; removed requirement of stim timing files", 7012 NULL 7013 } , 7014 7015 { 18, OCT, 2011, RCR, "@radial_correlate", MICRO, TYPE_ENHANCE, 7016 "require enough volumes per dataset, store file name correspondence", 7017 NULL 7018 } , 7019 7020 { 17, OCT, 2011, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 7021 "added -help for new -surf_* options, along with example #8", 7022 NULL 7023 } , 7024 7025 { 17, OCT, 2011, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 7026 "abin now has subdir (funstuff), so change 'mv' to 'rsync'", 7027 NULL 7028 } , 7029 7030 { 14, OCT, 2011, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 7031 "now processes surface data", 7032 "- added 'surf' processing block, and corresponding '-surf_*' options:\n" 7033 " -surf_anat, -surf_spec, -surf_anat_aligned, -surf_anat_has_skull,\n" 7034 " -surf_A, -surf_B, -surf_blur_fwhm\n" 7035 "- compute errts and TSNR by default (had required option or blur est)" 7036 } , 7037 7038 { 14, OCT, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7039 "small -help_install update", 7040 NULL 7041 } , 7042 7043 { 14, OCT, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 7044 "allow modest handling of surface results", 7045 NULL 7046 } , 7047 7048 { 6, OCT, 2011, RCR, "3dMean", MICRO, TYPE_BUG_FIX, 7049 "linux_xorg7_64 had optimizer error (and crashed), so altered loop method", 7050 "Thanks to P Kim for reporting the problem." 7051 } , 7052 7053 { 5, OCT, 2011, RCR, "uber_subject.py", MICRO, TYPE_BUG_FIX, 7054 "do not re-create proc script on proc execution", 7055 NULL 7056 } , 7057 7058 { 4, OCT, 2011, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 7059 "added -anat_has_skull option", 7060 NULL 7061 } , 7062 7063 { 4, OCT, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 7064 "changed basic script outputs", 7065 "- added 'max censored displacement', 'final anat dset' and\n" 7066 " 'final voxel resolution' to basic script\n" 7067 "- removed 'num stim files found'" 7068 } , 7069 7070 { 4, OCT, 2011, RCR, "to3d", MICRO, TYPE_MODIFY, 7071 "explicitly warn about illegal '/' characters in output filename", 7072 NULL 7073 } , 7074 7075 { 3, OCT, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7076 "changed default polort time back to TR*NT, to match 3dDeconvolve", 7077 NULL 7078 } , 7079 7080 { 3, OCT, 2011, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 7081 "added -censor_infile (e.g. to remove TRs from motion params)", 7082 "Added for N Adleman." 7083 } , 7084 7085 { 3, OCT, 2011, RCR, "afni-general", MICRO, TYPE_ENHANCE, 7086 "update ADN_ONE_STEP to ten million, allowing that many output sub-bricks", 7087 "This affects programs like 3dbucket, when the output has many volumes.\n" 7088 "Done for HJ Jo, J Gonzalez-Castillo, M Robinson." 7089 } , 7090 7091 { 22, SEP, 2011, RCR, "uber_ttest.py", MAJOR, TYPE_NEW_PROG, 7092 "a graphical program for running either 3dttest++ or 3dMEMA", 7093 "Still under destruction." 7094 } , 7095 7096 { 22, SEP, 2011, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 7097 "various updates", 7098 "- updated quotize_list\n" 7099 "- added nuke_final_whitespace, flist_to_table_pieces, get_ids_from_dsets" 7100 } , 7101 7102 { 22, SEP, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 7103 "added check_for_file and for_dset, updated find_x_mat, enorm, view_stats", 7104 NULL 7105 } , 7106 7107 { 22, SEP, 2011, RCR, "uber_align_test.py", MICRO, TYPE_MODIFY, 7108 "moved get_def_tool_path to library", 7109 NULL 7110 } , 7111 7112 { 22, SEP, 2011, RCR, "uber_subject.py", MINOR, TYPE_MODIFY, 7113 "altered spacing and made other minor changes", 7114 NULL 7115 } , 7116 7117 { 7, SEP, 2011, RCR, "Makefile.INCLUDE", MICRO, TYPE_MODIFY, 7118 "added @radial_correlate to the install scripts (forgot earlier)", 7119 NULL 7120 } , 7121 7122 { 6, SEP, 2011, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 7123 "added -fast option, short for: -sleep_init 50 -sleep_vol 50", 7124 NULL 7125 } , 7126 7127 { 1, SEP, 2011, RCR, "afni_util.py", MICRO, TYPE_BUG_FIX, 7128 "get_default_polort: run time should be TR * (NT-1)", 7129 "This was changed back to TR*NT, to match 3dDeconvolve (3 Oct, 2011)." 7130 } , 7131 7132 { 1, SEP, 2011, RCR, "@radial_correlate", MINOR, TYPE_NEW_PROG, 7133 "compute voxelwise EPI correlations with local spherical averages", 7134 NULL 7135 } , 7136 7137 { 31, AUG, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7138 "if censoring motion or outliers, add options to gen_ss_r command", 7139 NULL 7140 } , 7141 7142 { 30, AUG, 2011, RCR, "Dimon", MICRO, TYPE_BUG_FIX, 7143 "update volume delta to mean dz", 7144 "From text in DICOM files, initial dz values may not be sufficiently\n" 7145 "accurate, leaing to 'volume toasted' errors.\n" 7146 "Thanks to B Benson for reporting the problem." 7147 } , 7148 7149 { 19, AUG, 2011, RCR, "3dDeconvolve", MINOR, TYPE_MODIFY, 7150 "added the ability to output 1D sresp datasets", 7151 "Requested by S Baum." 7152 } , 7153 7154 { 17, AUG, 2011, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_BUG_FIX, 7155 "fixed some final anat dset assignments", 7156 NULL 7157 } , 7158 7159 { 15, AUG, 2011, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 7160 "altered SUMA_ParseFname for parsing of relative pathnames", 7161 "Thanks to Ryan of Princeton for reporting the problem." 7162 } , 7163 7164 { 12, AUG, 2011, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 7165 "gave volreg 3dAllineate command priority for final anat", 7166 NULL 7167 } , 7168 7169 { 4, AUG, 2011, RCR, "afni-general", MICRO, TYPE_MODIFY, 7170 "wrote loc_strcpy(/cat)_realloc for MCW_file_expand", 7171 "This is to allow for long sub-brick selectors." 7172 } , 7173 7174 { 3, AUG, 2011, RCR, "align_epi_anat.py", MICRO, TYPE_NEW_OPT, 7175 "added -save_orig_skullstrip, to avoid oblique transforms", 7176 "This was added for afni_proc.py." 7177 } , 7178 7179 { 3, AUG, 2011, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 7180 "changed aea.py -save_skullstrip to -save_orig_skullstrip", 7181 "The -save_skullstrip dataset might have an oblique transformation\n" 7182 "applied (which would throw off EPI if it is then sent to standard\n" 7183 "space). Apply the new option to grab a simple skull-stripped anat.\n" 7184 "Thanks to A Ellenstein for reporting it and Z Saad for help understanding." 7185 } , 7186 7187 { 2, AUG, 2011, RCR, "gen_ss_review_scripts.py", MICRO, TYPE_MODIFY, 7188 "added control var out_prefix, a prefix for output files", 7189 NULL 7190 } , 7191 7192 { 2, AUG, 2011, RCR, "uber_skel.py", MICRO, TYPE_MODIFY, 7193 "main class inherits object - for older versions of python", 7194 NULL 7195 } , 7196 7197 { 2, AUG, 2011, RCR, "uber_align_test.py", MICRO, TYPE_MODIFY, 7198 "main class inherits object - for older versions of python", 7199 NULL 7200 } , 7201 7202 { 29, JUL, 2011, RCR, "3dUniformize", MINOR, TYPE_BUG_FIX, 7203 "fixed checks against lower_limit in option processing (since -1 init)", 7204 "Thanks to A Waite for reporting the problem and cause in the code." 7205 } , 7206 7207 { 29, JUL, 2011, RCR, "make_pq_script.py", MINOR, TYPE_MODIFY, 7208 "changes to handle python 2.4, where shell output has extra blank lines", 7209 NULL 7210 } , 7211 7212 { 29, JUL, 2011, RCR, "slow_surf_clustsim.py", MINOR, TYPE_ENHANCE, 7213 "z.max files are now named by p-value", 7214 "And suggest a quick.alpha.vals.py command." 7215 } , 7216 7217 { 26, JUL, 2011, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 7218 "if e2a, update current anat to skull-stripped anat from align block", 7219 "This would avoid a second skull-strip step in @auto_tlrc." 7220 } , 7221 7222 { 25, JUL, 2011, RCR, "slow_surf_clustsim.py", MINOR, TYPE_ENHANCE, 7223 "added keepblocks var, to limit kept intermediate datasets", 7224 NULL 7225 } , 7226 7227 { 22, JUL, 2011, RCR, "slow_surf_clustsim.py", MINOR, TYPE_BUG_FIX, 7228 "after blur, rescale noise to be normally distributed", 7229 NULL 7230 } , 7231 7232 { 21, JUL, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_MODIFY, 7233 "changed TR counts to come via awk instead of grep", 7234 NULL 7235 } , 7236 7237 { 21, JUL, 2011, RCR, "edt_blur.c", MICRO, TYPE_BUG_FIX, 7238 "fixed nz/sigmay typo, found by Patryk (on message board)", 7239 NULL 7240 } , 7241 7242 { 20, JUL, 2011, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 7243 "fixed aea.py -epi_base when: aea.py, -volreg_a2 last, variable run lens", 7244 "thanks to S Brislin and S White for reporting the problem" 7245 } , 7246 7247 { 20, JUL, 2011, RCR, "make_pq_script.py", MINOR, TYPE_NEW_PROG, 7248 "program will generate a script to produce a p-value/q-value curve pair", 7249 NULL 7250 } , 7251 7252 { 15, JUL, 2011, RCR, "@update.afni.binaries", MICRO, TYPE_ENHANCE, 7253 "applied -d as -defaults", 7254 NULL 7255 } , 7256 7257 { 15, JUL, 2011, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 7258 "save output from ss_review in out.ss_review.$subj.txt", 7259 NULL 7260 } , 7261 7262 { 14, JUL, 2011, RCR, "gen_ss_review_scripts.py", MINOR, TYPE_ENHANCE, 7263 "added 'max motion displacement' to basic script", 7264 NULL 7265 } , 7266 7267 { 14, JUL, 2011, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 7268 "added -show_max_displace, for maximum motion displacement", 7269 NULL 7270 } , 7271 7272 { 14, JUL, 2011, RCR, "slow_surf_clustsim.py", MICRO, TYPE_ENHANCE, 7273 "show date per iter block and add ./ to 3dcalc prefix", 7274 NULL 7275 } , 7276 7277 { 13, JUL, 2011, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 7278 "run gen_ss_review_scripts.py and any resulting 'basic' review script", 7279 NULL 7280 } , 7281 7282 { 13, JUL, 2011, RCR, "gen_group_command.py", MICRO, TYPE_NEW_OPT, 7283 "added -exit0 and babbled about possible artifact tests", 7284 NULL 7285 } , 7286 7287 { 11, JUL, 2011, RCR, "gen_group_command.py", MINOR, TYPE_BUG_FIX, 7288 "fixed case of partial path match to dsets", 7289 "Problem found by J Jarcho." 7290 } , 7291 7292 { 11, JUL, 2011, RCR, "gen_ss_review_scripts.py", MAJOR, TYPE_NEW_PROG, 7293 "for generating single subject review scripts", 7294 "To be run by the afni_proc.py proc script or directly by users." 7295 } , 7296 7297 { 8, JUL, 2011, RCR, "slow_surf_clustsim.py", MINOR, TYPE_MODIFY, 7298 "added -on_surface, which might not end up being so useful", 7299 NULL 7300 } , 7301 7302 { 6, JUL, 2011, RCR, "uber_align_test.py", MICRO, TYPE_MODIFY, 7303 "test use of SUBJ.set_var_with_defs", 7304 NULL 7305 } , 7306 7307 { 6, JUL, 2011, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 7308 "create anat_final dset, as one that is aligned with the stats", 7309 "Also, suggest use of uber_subject.py in the -ask_me dialog." 7310 } , 7311 7312 { 5, JUL, 2011, RCR, "afni-general", MINOR, TYPE_ENHANCE, 7313 "minor enhancements to 5 python files (prep for gen_ss_review_scripts.py)", 7314 NULL 7315 } , 7316 7317 { 30, JUN, 2011, RCR, "afni_proc.c", MICRO, TYPE_MODIFY, 7318 "renamed aligned anat output (from align_epi_anat.py)", 7319 "This should make it clear whether or not the output anat should be used" 7320 } , 7321 7322 { 27, JUN, 2011, RCR, "gen_group_command.py", MINOR, TYPE_NEW_OPT, 7323 "added -dset_index0_list/-dset_index1_list options, etc.", 7324 "- ttest++ and MEMA commands now apply directories to datasets\n" 7325 "- changed Subject.atrs to be VarsObject instance, not dictionary\n" 7326 } , 7327 7328 { 27, JUN, 2011, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 7329 "changed decode_1D_ints to take imax param", 7330 "Affects 1d_tool.py, xmat_tool.py and any utilities using lib_afni1D.py.\n" 7331 "Also added restrict_by_index_lists()." 7332 } , 7333 7334 { 27, JUN, 2011, RCR, "thd_table.c", MICRO, TYPE_MODIFY, 7335 "output warning hint on single column covariate file", 7336 NULL 7337 } , 7338 7339 { 24, JUN, 2011, RCR, "slow_surf_clustsim.py", MAJOR, TYPE_NEW_PROG, 7340 "a temporary program until we do this in C", 7341 NULL 7342 } , 7343 7344 { 20, JUN, 2011, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 7345 "added eta2 function (alongside '3ddot -doeta2')", 7346 NULL 7347 } , 7348 7349 { 17, JUN, 2011, RCR, "SUMA_MiscFunc.c", MICRO, TYPE_BUG_FIX, 7350 "set 0-length BmP array to matching length 3", 7351 NULL 7352 } , 7353 7354 { 16, JUN, 2011, RCR, "3ddot", MINOR, TYPE_NEW_OPT, 7355 "added -doeta2 via new THD_eta_squared_masked", 7356 "Added for Shinchan." 7357 } , 7358 7359 { 16, JUN, 2011, RCR, "3dAutoTcorrelate", MICRO, TYPE_BUG_FIX, 7360 "allowed very small datasets", 7361 NULL 7362 } , 7363 7364 { 15, JUN, 2011, RCR, "gen_group_command.py", MINOR, TYPE_ENHANCE, 7365 "if constant dset names, extract SIDs from dir names", 7366 "Done for R Momenan." 7367 } , 7368 7369 { 8, JUN, 2011, RCR, "make_random_timing.py", MICRO, TYPE_BUG_FIX, 7370 "fixed print and added min_rest to durations in test of -tr_locked", 7371 NULL 7372 } , 7373 7374 { 3, JUN, 2011, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 7375 "added -volreg_compute_tsnr/-regress_compute_tsnr", 7376 "Volreg TSNR is no longer the default, but regress TSNR is." 7377 } , 7378 7379 { 3, JUN, 2011, RCR, "Makefile", MINOR, TYPE_NEW_OPT, 7380 "removed -lpng from Makefile.macosx_10.6_Intel_64", 7381 "We added -lpng because we were compiling our own OpenMotif\n" 7382 "(configure option?), but fink's version does not need it." 7383 } , 7384 7385 { 2, JUN, 2011, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 7386 "compute TSNR datasets (added -compute_tsnr); added -regress_make_cbucket", 7387 NULL 7388 } , 7389 7390 { 2, JUN, 2011, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 7391 "de-meaned motion regressors is now the default", 7392 "- added -regress_apply_mot_types to specify motion types for regression\n" 7393 "- added -regress_no_motion_demean and -regress_no_motion_deriv\n" 7394 "- by default, demean and deriv motion parameters are created\n" 7395 "- by default, demean motion parameters are applied in the regression\n" 7396 " (replacing the original 'basic' parameters, which should have no\n" 7397 " change in betas of interest, just the constant polort betas)" 7398 } , 7399 7400 { 27, MAY, 2011, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 7401 "re-work of motion, as prep for more motion options", 7402 "- replaced -volreg_regress_per_run with -regress_motion_per_run\n" 7403 "- made uniq_list_as_dsets() a warning, not an error (for J Britton)" 7404 } , 7405 7406 { 27, MAY, 2011, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 7407 "added -split_into_pad_runs (for regress motion per run)", 7408 NULL 7409 } , 7410 7411 { 25, MAY, 2011, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 7412 "added -global_to_local and -local_to_global for G Chen", 7413 NULL 7414 } , 7415 7416 { 24, MAY, 2011, RCR, "1dplot", MINOR, TYPE_BUG_FIX, 7417 "fixed plotting of varying length time series", 7418 NULL 7419 } , 7420 7421 { 20, MAY, 2011, RCR, "uber_subject.py", MINOR, TYPE_MODIFY, 7422 "execute via /usr/bin/env python", 7423 "Help now suggests fink as primary Mac source for PyQt4." 7424 } , 7425 7426 { 20, MAY, 2011, RCR, "uber_align_test.py", MINOR, TYPE_MODIFY, 7427 "execute via /usr/bin/env python", 7428 NULL 7429 } , 7430 7431 { 16, MAY, 2011, RCR, "uber_align_test.py", MINOR, TYPE_ENHANCE, 7432 "could be used as a release version", 7433 " - added 'check center dist' button, to display the current distance\n" 7434 " - added menu item to show afni command for viewing results\n" 7435 " - added menu items to show python and shell command windows\n" 7436 " - added much more help, including main and section buttons\n" 7437 " - added browsing of align_epi_anat.py help" 7438 } , 7439 7440 { 16, MAY, 2011, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 7441 "added exec_tcsh_command function", 7442 NULL 7443 } , 7444 7445 { 16, MAY, 2011, RCR, "@Center_Distance", MICRO, TYPE_ENHANCE, 7446 "return something to $status, so we can detect success or failure", 7447 NULL 7448 } , 7449 7450 { 13, MAY, 2011, RCR, "uber_align_test.py", MINOR, TYPE_ENHANCE, 7451 "added working GUI (for options, GUI help still needs ... help)", 7452 NULL 7453 } , 7454 7455 { 12, MAY, 2011, RCR, "uber_skel.py", MAJOR, TYPE_NEW_PROG, 7456 "A working skeleton for future uber programs.", 7457 "This is based on uber_align_test.py, version 0.2." 7458 } , 7459 7460 { 12, MAY, 2011, RCR, "uber_align_test.py", MINOR, TYPE_ENHANCE, 7461 "many small updates", 7462 "This set of 3 files was broken off set uber_skel.py, meant to be a\n" 7463 "resonable starting point for future uber programs." 7464 } , 7465 7466 { 11, MAY, 2011, RCR, "uber_align_test.py", MAJOR, TYPE_ENHANCE, 7467 "added basic graphical interface, still need to add variable fields", 7468 "o also made single cost_list\n" 7469 "o also added -help_howto_program, which might move to a skeleton program" 7470 } , 7471 7472 { 11, MAY, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7473 "small help/todo update", 7474 NULL 7475 } , 7476 7477 { 9, MAY, 2011, RCR, "to3d", MICRO, TYPE_ENHANCE, 7478 "applied formal parsing for CSA Image Header Info for Siemens slice timing", 7479 "Process field (0x0029 1010) as little-endian CSA1 or 2 header, tags\n" 7480 "and items. Get slice times from MosaicRefAcqTimes item.\n" 7481 "Thanks to I Souheil for finding NiBabel CSA format description." 7482 } , 7483 7484 { 4, MAY, 2011, RCR, "to3d", MICRO, TYPE_BUG_FIX, 7485 "fixed case of simult tpattern (so time_dep, but ui.tpattern is not set)", 7486 "Problem noted by J Ostuni." 7487 } , 7488 7489 { 2, MAY, 2011, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 7490 "added nul-termination and a.b[.d]+ rules for checking Siemens slice times", 7491 "Problem noted by D Kravitz and S Lee." 7492 } , 7493 7494 { 29, APR, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7495 "check that processing blocks are unique", 7496 NULL 7497 } , 7498 7499 { 28, APR, 2011, RCR, "uber_align_test.py", MAJOR, TYPE_NEW_PROG, 7500 "for testing EPI/anat alignment with various align_epi_anat.py options", 7501 "This is a command-line version, with a GUI to come soon." 7502 } , 7503 7504 { 28, APR, 2011, RCR, "uber_subject.py", MINOR, TYPE_NEW_OPT, 7505 "reconcile LUS.py with LS.py in prep for uber_align_test.py", 7506 NULL 7507 } , 7508 7509 { 28, APR, 2011, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 7510 "added -align_epi_strip_method", 7511 NULL 7512 } , 7513 7514 { 25, APR, 2011, RCR, "Imon", MINOR, TYPE_MODIFY, 7515 "Imon is getting phased out of the distribution (see 'Dimon -use_imon')", 7516 "Requires compiling alterations to be put back in (if anyone wants it)." 7517 } , 7518 7519 { 25, APR, 2011, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 7520 "have Dimon send 'TPATTERN explicit' with slice timing to RT plugin", 7521 NULL 7522 } , 7523 7524 { 24, APR, 2011, RCR, "@Align_Centers", MINOR, TYPE_ENHANCE, 7525 "allow -base dset to be in PATH, AFNI_PLUGINPATH, etc.", 7526 NULL 7527 } , 7528 7529 { 22, APR, 2011, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 7530 "if manual tlrc and -volreg_tlrc_adwarp, also transform extents mask", 7531 "Noted by J Britton.\n" 7532 "Also, if -regress_reml_exec, insert 3dClustSim table in stats_REML.\n" 7533 "Noted by R Momenan." 7534 } , 7535 7536 { 15, APR, 2011, RCR, "Dimon", MINOR, TYPE_ENHANCE, 7537 "added FROM_IMAGE as default Siemens slice pattern in to3d command", 7538 NULL 7539 } , 7540 7541 { 15, APR, 2011, RCR, "dicom_hdr", MINOR, TYPE_NEW_OPT, 7542 "added -slice_times and -slice_times_verb, to show siemens slice timing", 7543 NULL 7544 } , 7545 7546 { 14, APR, 2011, RCR, "thd_atlas.c", MICRO, TYPE_BUG_FIX, 7547 "for solaris, apply #def strcasestr strstr", 7548 NULL 7549 } , 7550 7551 { 13, APR, 2011, RCR, "to3d", MINOR, TYPE_NEW_OPT, 7552 "added FROM_IMAGE timing pattern (for Siemens mosaic images)", 7553 NULL 7554 } , 7555 7556 { 11, APR, 2011, RCR, "uber_subject.py", MICRO, TYPE_BUG_FIX, 7557 "fixed lost warnings for no sid/gid", 7558 NULL 7559 } , 7560 7561 { 8, APR, 2011, RCR, "Makefile", MICRO, TYPE_MODIFY, 7562 "removed -lf2c from Makefile.INCLUDE, added to LLIBS in Makefile.*", 7563 "Also removed redundant -lmri from many Makefiles and Makefile.INCLUDE." 7564 } , 7565 7566 { 7, APR, 2011, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 7567 "backports for Ubuntu 9", 7568 "requested by J Bodurka" 7569 } , 7570 7571 { 6, APR, 2011, RCR, "uber_subject.py", MICRO, TYPE_MODIFY, 7572 "make table size depend on font", 7573 NULL 7574 } , 7575 7576 { 5, APR, 2011, RCR, "howto", MINOR, TYPE_ENHANCE, 7577 "updated the class setup and basic Linux instructions for PyQt4", 7578 NULL 7579 } , 7580 7581 { 5, APR, 2011, RCR, "python_module_test.py", MICRO, TYPE_NEW_OPT, 7582 "added PyQt4 to test list", 7583 NULL 7584 } , 7585 7586 { 29, MAR, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7587 "changed subject directory to group.GROUP/subj.SUBJ", 7588 NULL 7589 } , 7590 7591 { 24, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7592 "added align and tlrc option boxes, adjusted spacing", 7593 NULL 7594 } , 7595 7596 { 23, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7597 "moved gltsym box to below stim, save AP output, small mac install update", 7598 NULL 7599 } , 7600 7601 { 22, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7602 "processing status, clear options/fields menu items, etc...", 7603 NULL 7604 } , 7605 7606 { 22, MAR, 2011, RCR, "to3d", MINOR, TYPE_BUG_FIX, 7607 "mri_read_dicom: if there is no vrCode, skip explicitVR", 7608 NULL 7609 } , 7610 7611 { 21, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7612 "many updates, including extra regress options box", 7613 NULL 7614 } , 7615 7616 { 20, MAR, 2011, RCR, "uber_subject.py", MAJOR, TYPE_ENHANCE, 7617 "handle symbolic GLTs, etc.", 7618 NULL 7619 } , 7620 7621 { 15, MAR, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7622 "changed uncensored Xmat to X.nocensor.1D", 7623 NULL 7624 } , 7625 7626 { 15, MAR, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7627 "added -regress_make_ideal_sum, subject variables, GUI text changes", 7628 NULL 7629 } , 7630 7631 { 14, MAR, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7632 "if no mask but extents, apply in scale step", 7633 NULL 7634 } , 7635 7636 { 14, MAR, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7637 "a handful of minor updates", 7638 NULL 7639 } , 7640 7641 { 9, MAR, 2011, RCR, "uber_subject.py", MICRO, TYPE_ENHANCE, 7642 "updates to uber_subject.py, how could I possibly remember what they are...", 7643 NULL 7644 } , 7645 7646 { 9, MAR, 2011, RCR, "make_random_timing.py", MICRO, TYPE_BUG_FIX, 7647 "fixed bug writing comment text in 3dD script", 7648 "Problem noted by Z Saad and P Kaskan." 7649 } , 7650 7651 { 8, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7652 "uber_subject.py command menu item, ...", 7653 NULL 7654 } , 7655 7656 { 7, MAR, 2011, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 7657 "make proc script executable", 7658 NULL 7659 } , 7660 7661 { 7, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7662 "updates: command and pycommand windows, new Process classes, ...", 7663 NULL 7664 } , 7665 7666 { 3, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7667 "updates: control vars, subj dir, view actions, result vars, ...", 7668 NULL 7669 } , 7670 7671 { 2, MAR, 2011, RCR, "uber_subject.py", MINOR, TYPE_ENHANCE, 7672 "many updates, including write and exec of proc script", 7673 "There is still much to do before first release version." 7674 } , 7675 7676 { 22, FEB, 2011, RCR, "uber_subject.py", MINOR, TYPE_MODIFY, 7677 "added interfaces for 'expected' option", 7678 NULL 7679 } , 7680 7681 { 17, FEB, 2011, RCR, "3dDeconvolve", MICRO, TYPE_MODIFY, 7682 "make -CENSORTR run: warning more clear", 7683 NULL 7684 } , 7685 7686 { 17, FEB, 2011, RCR, "3dROIstats", MICRO, TYPE_MODIFY, 7687 "make unknown option error more clear", 7688 NULL 7689 } , 7690 7691 { 16, FEB, 2011, RCR, "uber_subject.py", MINOR, TYPE_MODIFY, 7692 "epi or stim list from command line can init order/labels; file reorg", 7693 "Also, initiated regression testing tree." 7694 } , 7695 7696 { 16, FEB, 2011, RCR, "howto", MINOR, TYPE_MODIFY, 7697 "updated the main page and basic Linux instructions", 7698 NULL 7699 } , 7700 7701 { 15, FEB, 2011, RCR, "uber_subject.py", SUPER, TYPE_NEW_PROG, 7702 "added CLI (command-line interface), generates basic afni_proc.py script", 7703 "Many enhancements yet to come." 7704 } , 7705 7706 { 14, FEB, 2011, RCR, "uber_proc.py", MINOR, TYPE_GENERAL, 7707 "moved uber program into main repository", 7708 NULL 7709 } , 7710 7711 { 12, FEB, 2011, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 7712 "updates for uber_subject.py", 7713 NULL 7714 } , 7715 7716 { 11, FEB, 2011, RCR, "lib_subjects.py", MICRO, TYPE_ENHANCE, 7717 "more updates for uber_subject.py", 7718 NULL 7719 } , 7720 7721 { 1, FEB, 2011, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 7722 "updates for parsing a stim file list", 7723 NULL 7724 } , 7725 7726 { 31, JAN, 2011, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 7727 "updates for uber_subj.py", 7728 NULL 7729 } , 7730 7731 { 25, JAN, 2011, RCR, "lib_subjects.py", MICRO, TYPE_ENHANCE, 7732 "updates to the VarsObject class", 7733 NULL 7734 } , 7735 7736 { 19, JAN, 2011, RCR, "lib_subjects.py", MINOR, TYPE_ENHANCE, 7737 "many updates to the VarsObject class", 7738 NULL 7739 } , 7740 7741 { 13, JAN, 2011, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7742 "small changes to warnings for missing stimulus files", 7743 NULL 7744 } , 7745 7746 { 13, JAN, 2011, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 7747 "added -gert_write_as_nifti and -gert_create_dataset", 7748 "requested by V Roopchansingh" 7749 } , 7750 7751 { 10, JAN, 2011, RCR, "3dttest", MICRO, TYPE_GENERAL, 7752 "fail with error message when -set2 is not the final option", 7753 "It had already been assumed to be the final option." 7754 } , 7755 7756 { 7, JAN, 2011, RCR, "rickr/Makefile", MICRO, TYPE_BUG_FIX, 7757 "Dimon: forgot to reconcile use of expat (with LGIFTI)", 7758 NULL 7759 } , 7760 7761 { 6, JAN, 2011, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 7762 "ComputeObliquity() mosaic shift should be dcK*(nK-1)/2 in each direction", 7763 NULL 7764 } , 7765 7766 { 4, JAN, 2011, RCR, "Dimon", MAJOR, TYPE_ENHANCE, 7767 "version 3.0 : handle Siemens Mosaic formatted files", 7768 "- depend on libmri, return MRI_IMARR from mri_read_dicom, changes\n" 7769 " for oblique and mosaic processing\n" 7770 "- mri_read_dicom.c: g_info (process control), g_image_info (Dimon)\n" 7771 " replaced DEBUG_ON/debugprint with g_info.verb, many small changes\n" 7772 "- mri_dicom_elist.h: merged with dimon_afni.h\n" 7773 "- mcw_glob.[ch]: control sort direction via rglob_set_sort_dir()" 7774 } , 7775 7776 { 4, JAN, 2011, RCR, "afni", MICRO, TYPE_GENERAL, 7777 "do not open default windows in case of real-time", 7778 NULL 7779 } , 7780 7781 { 23, DEC, 2010, RCR, "to3d", MINOR, TYPE_NEW_OPT, 7782 "added -use_old_mosaic_code", 7783 "This is phase 1 of dealing with Siemens mosaic format in Dimon.\n" 7784 "Siemens mosaic functions we moved to new mri_process_siemens.c,\n" 7785 "with the ability to use the old code preserved with this option." 7786 } , 7787 7788 { 16, DEC, 2010, RCR, "@ANATICOR", MICRO, TYPE_GENERAL, 7789 "HJ change: small updates to the help", 7790 "changes were submitted for Hang Joon Jo" 7791 } , 7792 7793 { 16, DEC, 2010, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 7794 "updates to file type (looks like) errors and warnings", 7795 NULL 7796 } , 7797 7798 { 16, DEC, 2010, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 7799 "updates to file type (looks like) errors and warnings", 7800 NULL 7801 } , 7802 7803 { 15, DEC, 2010, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 7804 "use lib_textdata.py for reading timing files, allow empty file", 7805 "empty file update for C Deveney" 7806 } , 7807 7808 { 14, DEC, 2010, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 7809 "fixed problem with timing file tests on 'empty' files with '*'", 7810 "problem noted by C Deveney and R Momenan" 7811 } , 7812 7813 { 30, NOV, 2010, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 7814 "added option -final_sort_by_prog", 7815 NULL 7816 } , 7817 7818 { 22, NOV, 2010, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 7819 "small improvements to line wrapping", 7820 NULL 7821 } , 7822 7823 { 19, NOV, 2010, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 7824 "add -write_all_rest_times, moved write_to_timing_file to afni_util.py", 7825 "option added for J Poore" 7826 } , 7827 7828 { 18, NOV, 2010, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 7829 "fixed stim_files to stim_times conversion after multi_basis change", 7830 "problem noted by M Weber" 7831 } , 7832 7833 { 18, NOV, 2010, RCR, "make_stim_times.py", MICRO, TYPE_BUG_FIX, 7834 "fix for '*' in max 1 stim per run case", 7835 NULL 7836 } , 7837 7838 { 10, NOV, 2010, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 7839 "added new NOTE sections for ANAT/EPI ALIGNMENT to -help output", 7840 NULL 7841 } , 7842 7843 { 8, NOV, 2010, RCR, "gen_group_command.py", MAJOR, TYPE_NEW_OPT, 7844 "can now generate 3dttest++ commands", 7845 NULL 7846 } , 7847 7848 { 4, NOV, 2010, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7849 "use X.uncensored.xmat.1D instead of X.full_length.xmat.1D", 7850 NULL 7851 } , 7852 7853 { 4, NOV, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 7854 "added regress_basis_multi, -regress_no_ideal_sum", 7855 "One can specify either one basis function or one per stim_times file." 7856 } , 7857 7858 { 4, NOV, 2010, RCR, "1d_tool.py", MICRO, TYPE_BUG_FIX, 7859 "fixed print problem in -show_indices", 7860 "Problem noted by Mingbo Cai." 7861 } , 7862 7863 { 2, NOV, 2010, RCR, "3dTstat", MINOR, TYPE_ENHANCE, 7864 "allow single volume input for functions mean, max, min, sum", 7865 "Other functions can be added to this list as needed." 7866 } , 7867 7868 { 29, OCT, 2010, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 7869 "added -show_indices_baseline, _motion and _interest", 7870 NULL 7871 } , 7872 7873 { 28, OCT, 2010, RCR, "3dMean", MICRO, TYPE_BUG_FIX, 7874 "do not proceed in case of no input datasets", 7875 NULL 7876 } , 7877 7878 { 27, OCT, 2010, RCR, "file_tool", MINOR, TYPE_NEW_OPT, 7879 "added -show_bad_char and -show_bad_all", 7880 NULL 7881 } , 7882 7883 { 26, OCT, 2010, RCR, "gen_group_command.py", MINOR, TYPE_NEW_OPT, 7884 "solidified 3dMEMA commands", 7885 "This is now used to generate AFNI_data6/group_results/s4.3dMEMA.V-A." 7886 } , 7887 7888 { 25, OCT, 2010, RCR, "gen_group_command.py", MAJOR, TYPE_NEW_PROG, 7889 "a program to generate group commands (3dMEMA for now)", 7890 "Commands to come: 3dttest(++), 3dANOVA*, GroupANA." 7891 } , 7892 7893 { 21, OCT, 2010, RCR, "timing_tool.py", MICRO, TYPE_NEW_OPT, 7894 "added -shift_to_run_offset", 7895 NULL 7896 } , 7897 7898 { 20, OCT, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 7899 "added -tcat_remove_last_trs, -ricor_regs_rm_nlast", 7900 "Added for J Czarapata." 7901 } , 7902 7903 { 20, OCT, 2010, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 7904 "added -sort_by_acq_time for -dicom_org on Philips data", 7905 "Added for Manjula." 7906 } , 7907 7908 { 20, OCT, 2010, RCR, "thd_niftiwrite.c", MICRO, TYPE_BUG_FIX, 7909 "brick stats to intent codes was off by 1 index", 7910 "Problem noted by P Kohn." 7911 } , 7912 7913 { 16, OCT, 2010, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 7914 "fixed timing_to_1D fractions", 7915 NULL 7916 } , 7917 7918 { 15, OCT, 2010, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 7919 "added -multi_timing_to_events, -multi_timing_to_event_pair, -per_run", 7920 "- Modified timing_tool.py, lib_timing.py, lib_textdata.py, afni_util.py.\n" 7921 "- Added for N Adleman." 7922 } , 7923 7924 { 12, OCT, 2010, RCR, "3dREMLfit", MICRO, TYPE_GENERAL, 7925 "small help update to clarify slice-based regressor warnings", 7926 "Requested by D Handwerker." 7927 } , 7928 7929 { 17, SEP, 2010, RCR, "3dttest++", MINOR, TYPE_BUG_FIX, 7930 "init workspace with 0", 7931 "Trouble noted by M Choi" 7932 } , 7933 7934 { 10, SEP, 2010, RCR, "@SUMA_Make_Spec_FS", MICRO, TYPE_BUG_FIX, 7935 "removed extra endif's in case of $label_dir", 7936 NULL 7937 } , 7938 7939 { 8, SEP, 2010, RCR, "afni_util.py", MICRO, TYPE_ENHANCE, 7940 "added wildcard construction functions", 7941 NULL 7942 } , 7943 7944 { 1, SEP, 2010, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 7945 "tiny changes to help output (e.g. 3dAllineate options)", 7946 NULL 7947 } , 7948 7949 { 30, AUG, 2010, RCR, "3dVol2Surf", MICRO, TYPE_BUG_FIX, 7950 "check for -sv dataset before proceeding", 7951 NULL 7952 } , 7953 7954 { 30, AUG, 2010, RCR, "@CheckForAfniDset", MICRO, TYPE_BUG_FIX, 7955 "replaced use of {$var} with ${var}", 7956 "Problem noted by R Mruczek." 7957 } , 7958 7959 { 25, AUG, 2010, RCR, "make_random_timing.py", MICRO, TYPE_MODIFY, 7960 "update polort and write -nodata TR using 3 decimal places", 7961 NULL 7962 } , 7963 7964 { 18, AUG, 2010, RCR, "@build_afni_Xlib", MICRO, TYPE_NEW_OPT, 7965 "added -lib32 for building 32-bit on a 64-bit Linux box", 7966 NULL 7967 } , 7968 7969 { 18, AUG, 2010, RCR, "afni-general", MINOR, TYPE_MODIFY, 7970 "changed Makefile.linux_openmp (and _64) building on F10 (was F12)", 7971 NULL 7972 } , 7973 7974 { 17, AUG, 2010, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 7975 "allowed married timing files", 7976 "Also, delete output script on failure (have -keep_script_on_err option)." 7977 } , 7978 7979 { 16, AUG, 2010, RCR, "lib_textdata.py", MINOR, TYPE_ENHANCE, 7980 "new module to deal with reading/writing 1D/timing/married text files", 7981 "heading towards handling married timing in afni_proc.py" 7982 } , 7983 7984 { 16, AUG, 2010, RCR, "make_stim_times.py", MICRO, TYPE_MODIFY, 7985 "use lib_textdata.py for I/O", 7986 NULL 7987 } , 7988 7989 { 16, AUG, 2010, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 7990 "use lib_textdata.py for I/O", 7991 NULL 7992 } , 7993 7994 { 16, AUG, 2010, RCR, "lib_afni1D.py", MICRO, TYPE_MODIFY, 7995 "use lib_textdata.py for I/O (deleted read_1D_file)", 7996 NULL 7997 } , 7998 7999 { 16, AUG, 2010, RCR, "afni_xmat.py", MICRO, TYPE_MODIFY, 8000 "use lib_textdata.py for I/O (deleted read_1D_file)", 8001 NULL 8002 } , 8003 8004 { 16, AUG, 2010, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 8005 "rewrote and moved text data I/O routines into lib_textdata.py", 8006 NULL 8007 } , 8008 8009 { 13, AUG, 2010, RCR, "Makefile.INCLUDE", MICRO, TYPE_GENERAL, 8010 "explicitly link the math library for the balloon target", 8011 NULL 8012 } , 8013 8014 { 5, AUG, 2010, RCR, "afni-general", MICRO, TYPE_GENERAL, 8015 "do not let THD_write_3dim_dataset fail silently", 8016 NULL 8017 } , 8018 8019 { 4, AUG, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8020 "added -regress_CS_NN, default to 123", 8021 "Also, changed -niml to -both so that 1D files are output, and changed\n" 8022 "the prefix to ClustSim (from rm.CS) so those files are not deleted.\n" 8023 "If ClustSim is explicitly requested, require blur estimation." 8024 } , 8025 8026 { 3, AUG, 2010, RCR, "afni_history", MICRO, TYPE_BUG_FIX, 8027 "fixed -check_date test to see if version is current", 8028 "This problem affects afni_proc.py script execution." 8029 } , 8030 8031 { 2, AUG, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8032 "check that stim_file/_time files match datasets, and that dsets exist", 8033 "- default is to check that files are appropriate for the input data\n" 8034 "- default is to check that input datasets exist\n" 8035 "- added options -test_stim_files and -test_for_dsets\n" 8036 "- afni_proc.py now depends on lib_afni1D" 8037 } , 8038 8039 { 2, AUG, 2010, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 8040 "small looks_like text change and remove TR from look_like_1D", 8041 NULL 8042 } , 8043 8044 { 30, JUL, 2010, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 8045 "added options to evaluate whether a file is valid as 1D or stim_times", 8046 "Added -looks_like_1D, -looks_like_local_times, -looks_like_global_times\n" 8047 "and -looks_like_test_all.\n" 8048 "The main purpose is to have tests that afni_proc.py can apply." 8049 } , 8050 8051 { 28, JUL, 2010, RCR, "zfun.c", MICRO, TYPE_BUG_FIX, 8052 "fixed small typos in the case of HAVE_ZLIB not being defined", 8053 "- zzb64_to_array (return) and array_to_zzb64 (missing arg)" 8054 } , 8055 8056 { 27, JUL, 2010, RCR, "thd_table.c", MICRO, TYPE_BUG_FIX, 8057 "strtod typo", 8058 NULL 8059 } , 8060 8061 { 27, JUL, 2010, RCR, "afni-general", MINOR, TYPE_ENHANCE, 8062 "propagate storage_mode in THD_open_tcat", 8063 "This is for non-AFNI formatted datasets, and fixes the problem where\n" 8064 "3dDeconvolve would not propagate nnodes/node_list of surface datasets.\n" 8065 "Problem noted by N Oosterhof." 8066 } , 8067 8068 { 23, JUL, 2010, RCR, "afni-general", MINOR, TYPE_ENHANCE, 8069 "added Makefile.linux_openmp (and _64) for building with OpenMP support", 8070 "Those distribution binaries will be built on a 64-bit Fedora 12 system." 8071 } , 8072 8073 { 22, JUL, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8074 "added options -regress_run_clustsim and -regress_opts_CS", 8075 "This is to apply 3dClustSim results for multiple comparison correction\n" 8076 "to the stats dataset output from 3dDeconvolve." 8077 } , 8078 8079 { 20, JUL, 2010, RCR, "xmat_tool.py", MICRO, TYPE_MODIFY, 8080 "made small improvement out text formatting for cormat and cosmat", 8081 NULL 8082 } , 8083 8084 { 19, JUL, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8085 "added -check_afni_version and -requires_afni_version", 8086 "This will allow the processing script to verify that the AFNI version\n" 8087 "is recent enough for the enclosed commands." 8088 } , 8089 8090 { 19, JUL, 2010, RCR, "@DriveAfni", MICRO, TYPE_NEW_OPT, 8091 "added -help", 8092 NULL 8093 } , 8094 8095 { 19, JUL, 2010, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 8096 "added -check_date, to verify whether the distribution is current", 8097 NULL 8098 } , 8099 8100 { 19, JUL, 2010, RCR, "3dFWHMx", MICRO, TYPE_BUG_FIX, 8101 "fixed -arith mean", 8102 NULL 8103 } , 8104 8105 { 16, JUL, 2010, RCR, "afni", MICRO, TYPE_BUG_FIX, 8106 "added legendre to forced_loads array for plugin use", 8107 NULL 8108 } , 8109 8110 { 16, JUL, 2010, RCR, "3dMean", MINOR, TYPE_NEW_OPT, 8111 "added -mask_union and -mask_inter, for creation of mask datasets", 8112 NULL 8113 } , 8114 8115 { 14, JUL, 2010, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 8116 "added -mask_test_overlap and -regress_cormat_warnigns", 8117 "Unless the user sets these options to 'no', the processing script\n" 8118 "will now use 3dABoverlap to evaluate the anat/EPI mask overlap, and\n" 8119 "1d_tool.py to check the X-matrix for large pairwise correlations\n" 8120 "between any two regressors." 8121 } , 8122 8123 { 14, JUL, 2010, RCR, "3dABoverlap", MICRO, TYPE_ENHANCE, 8124 "added -no_automask to allow mask datasets as input", 8125 NULL 8126 } , 8127 8128 { 14, JUL, 2010, RCR, "Makefile.linux_gcc33_64", MICRO, TYPE_MODIFY, 8129 "use staic link of SUMA programs to Motif, as AFNI programs already do", 8130 NULL 8131 } , 8132 8133 { 13, JUL, 2010, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 8134 "added channel list selection, for choosing which channels to merge", 8135 NULL 8136 } , 8137 8138 { 12, JUL, 2010, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 8139 "added -truncate_times and -round_times for S Durgerian", 8140 NULL 8141 } , 8142 8143 { 11, JUL, 2010, RCR, "timing_tool.py", MINOR, TYPE_ENHANCE, 8144 "show TR offset stats if -tr and -show_isi_stats", 8145 NULL 8146 } , 8147 8148 { 7, JUL, 2010, RCR, "NIFTI", MICRO, TYPE_BUG_FIX, 8149 "fixed znzread/write to again return nmembers", 8150 "Also, added M Hanke's update to CMakeLists.txt for new realease number." 8151 } , 8152 8153 { 7, JUL, 2010, RCR, "nifti_tool", MICRO, TYPE_BUG_FIX, 8154 "fixed nt_read_bricks bsize computation for large files", 8155 NULL 8156 } , 8157 8158 { 7, JUL, 2010, RCR, "NIFTI", MINOR, TYPE_BUG_FIX, 8159 "fixes for large files (noted/investigated by M Hanke and Y Halchenko)", 8160 "- fixed znzread/write, noting example by M Adler\n" 8161 "- changed nifti_swap_* routines/calls to take size_t" 8162 } , 8163 8164 { 28, JUN, 2010, RCR, "GIFTI", MICRO, TYPE_ENHANCE, 8165 "applied CMakeLists.txt update from M Hanke for Debian release", 8166 NULL 8167 } , 8168 8169 { 28, JUN, 2010, RCR, "GIFTI", MICRO, TYPE_MODIFY, 8170 "the most significant dimension cannot be 1", 8171 "Requested by N Schmansky" 8172 } , 8173 8174 { 28, JUN, 2010, RCR, "3dAutoTcorrelate", MINOR, TYPE_NEW_OPT, 8175 "added -eta2 (Cohen eta squared) for HJ Jo", 8176 "Also added -mask and -mask_only_targets." 8177 } , 8178 8179 { 22, JUN, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8180 "3dToutcount detrending now defaults to Legendre polynomials", 8181 " Using Legendre polynomials, 3dToutcount polort can exceed 3\n" 8182 " (limit noted by I Mukai and K Bahadur).\n" 8183 " Added options -outlier_legendre and -outlier_polort." 8184 } , 8185 8186 { 22, JUN, 2010, RCR, "3dToutcount", MINOR, TYPE_NEW_OPT, 8187 "added -legendre option, which also allows polort > 3", 8188 NULL 8189 } , 8190 8191 { 17, JUN, 2010, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 8192 "apply default polort in 3dToutcount", 8193 NULL 8194 } , 8195 8196 { 17, JUN, 2010, RCR, "3dTcat", MICRO, TYPE_ENHANCE, 8197 "removed sub-brick length limit", 8198 NULL 8199 } , 8200 8201 { 10, JUN, 2010, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 8202 "fixed copying EPI and anat as NIFTI", 8203 NULL 8204 } , 8205 8206 { 8, JUN, 2010, RCR, "timing_tool.py", MICRO, TYPE_BUG_FIX, 8207 "fixed partitioning without zeros", 8208 NULL 8209 } , 8210 8211 { 8, JUN, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8212 "added -regress_censor_outliers and -regress_skip_first_outliers", 8213 NULL 8214 } , 8215 8216 { 4, JUN, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8217 "moved outlier counting outside of tshift block", 8218 "- if only one regressor, use 1dcat for 'sum' ideal\n" 8219 "- added -count_outliers, default to 'yes'\n" 8220 "- outlier counting is now at end of tcat block" 8221 } , 8222 8223 { 4, JUN, 2010, RCR, "3dToutcount", MICRO, TYPE_NEW_OPT, 8224 "added -fraction to output fraction of bad voxels, instead of count", 8225 "This will be used by afni_proc.py for censoring." 8226 } , 8227 8228 { 3, JUN, 2010, RCR, "plug_realtime", MAJOR, TYPE_ENHANCE, 8229 "added ability to register merged data and possibly all channels", 8230 "Via MergeRegister, one can request to register the ChannelMerge dataset.\n" 8231 "The individual channels can also be 'registered' via the same parameters\n" 8232 "as the ChannelMerge dataset.\n" 8233 "Requested by J Hyde, A Jesmanowicz, D Ward of MCW." 8234 } , 8235 8236 { 3, JUN, 2010, RCR, "afni_history", MICRO, TYPE_ENHANCE, 8237 "added TYPE_ENHANCE, often a more appropriate term", 8238 NULL 8239 } , 8240 8241 { 1, JUN, 2010, RCR, "afni_util.py", MINOR, TYPE_ENHANCE, 8242 "added variance and t-test routines (1-sample, paired, pooled, unpooled)", 8243 NULL 8244 } , 8245 8246 { 27, MAY, 2010, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 8247 "fixed use of -volreg_regress_per_run and -regress_censor_motion pair", 8248 "Problem found by D Drake." 8249 } , 8250 8251 { 20, MAY, 2010, RCR, "Makefile.NIH.CentOS.5.3_64", MICRO, TYPE_MODIFY, 8252 "update CCOLD to compile with gcc verion 3.4", 8253 NULL 8254 } , 8255 8256 { 19, MAY, 2010, RCR, "Makefile.*", MINOR, TYPE_BUG_FIX, 8257 "add CCOLD to all for compiling nifticdf.o on linux_xorg7_64 using gcc v3", 8258 "This is a bug in the gcc compiler code, not in AFNI. So the workaround\n" 8259 "is to compile nifticdf.o with a different version of the compiler.\n" 8260 "\n" 8261 "The gcc compiler versions 4.1-4.3 (at least) had an optimization bug\n" 8262 "when compiling nifticdf.o. The result was an inaccurate conversion\n" 8263 "from F-stats to p-values (in some cases).\n" 8264 "Test with the command: cdf -t2p fift 1.0 10 100\n" 8265 " good result: 0.448817, bad result: 0.0472392\n" 8266 "Problem found by L Thomas and B Bones." 8267 } , 8268 8269 { 13, MAY, 2010, RCR, "3dbucket", MICRO, TYPE_GENERAL, 8270 "tiny help update to clarify -glueto and -aglueto", 8271 NULL 8272 } , 8273 8274 { 13, MAY, 2010, RCR, "ui_xmat.py", MICRO, TYPE_GENERAL, 8275 "tiny update: check for set_afni_xmat() failure", 8276 NULL 8277 } , 8278 8279 { 12, MAY, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8280 "added -regress_censor_first_trs for A Barbey", 8281 "This is needed when also using -regress_censor_motion." 8282 } , 8283 8284 { 12, MAY, 2010, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 8285 "added -censor_first_trs, to mix with -censor_motion results", 8286 NULL 8287 } , 8288 8289 { 10, MAY, 2010, RCR, "ktaub.c", MICRO, TYPE_BUG_FIX, 8290 "allow for build on SOLARIS_OLD", 8291 NULL 8292 } , 8293 8294 { 6, MAY, 2010, RCR, "Dimon", MINOR, TYPE_ENHANCE, 8295 "allow negatives in -sort_by_num_suffix, look for '0054 1330' in sorting", 8296 NULL 8297 } , 8298 8299 { 1, MAY, 2010, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 8300 "added -max_consec for Liat of Cornell", 8301 NULL 8302 } , 8303 8304 { 29, APR, 2010, RCR, "@DriveAfni", MICRO, TYPE_ENHANCE, 8305 "minor updates", 8306 NULL 8307 } , 8308 8309 { 28, APR, 2010, RCR, "NIFTI", MICRO, TYPE_ENHANCE, 8310 "added NIFTI_ECODE_CARET for J. Harwell", 8311 NULL 8312 } , 8313 8314 { 26, APR, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8315 "added -regress_opts_reml", 8316 NULL 8317 } , 8318 8319 { 26, APR, 2010, RCR, "3dDeconvolve", MINOR, TYPE_ENHANCE, 8320 "add $* to end of 3dREMLfit script command, for additional arguments", 8321 "Finally getting around to afni_proc.py option -regress_opts_reml..." 8322 } , 8323 8324 { 28, MAR, 2010, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 8325 "applied fitts computation to REML case", 8326 NULL 8327 } , 8328 8329 { 25, MAR, 2010, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 8330 "small help update", 8331 NULL 8332 } , 8333 8334 { 25, MAR, 2010, RCR, "afni_proc.py", MICRO, TYPE_ENHANCE, 8335 "small help update describing help sections", 8336 NULL 8337 } , 8338 8339 { 25, MAR, 2010, RCR, "plug_crender", MICRO, TYPE_GENERAL, 8340 "changed name in plugin list to original 'Render Dataset'", 8341 "Also changed plug_render to 'Render [old]', though it is no longer\n" 8342 "built by default." 8343 } , 8344 8345 { 25, MAR, 2010, RCR, "3dcopy", MICRO, TYPE_GENERAL, 8346 "on failure, warn user that sub-brick selection is not allowed", 8347 "Requested by T Nycum." 8348 } , 8349 8350 { 23, MAR, 2010, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8351 "added -regress_compute_fitts option, to save memory in 3dDeconvolve", 8352 NULL 8353 } , 8354 8355 { 19, MAR, 2010, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 8356 "round to 3 bits below 4 (above, truncate to int)", 8357 NULL 8358 } , 8359 8360 { 19, MAR, 2010, RCR, "3dfractionize", MICRO, TYPE_GENERAL, 8361 "added 3dAllineate example of inverse tlrc warp", 8362 NULL 8363 } , 8364 8365 { 18, MAR, 2010, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 8366 "handle args with '\\n' in them (probably from quoted newlines)", 8367 NULL 8368 } , 8369 8370 { 18, MAR, 2010, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 8371 "small updates to help for alignment options", 8372 NULL 8373 } , 8374 8375 { 17, MAR, 2010, RCR, "timing_tool.py", MINOR, TYPE_BUG_FIX, 8376 "fixed timing_to_1D when some runs are empty", 8377 "Problem found by L Thomas and B Bones." 8378 } , 8379 8380 { 16, MAR, 2010, RCR, "3dAttribute", MICRO, TYPE_ENHANCE, 8381 "set_dataset_attributes() on read - so can use on non-AFNI datasets", 8382 NULL 8383 } , 8384 8385 { 16, MAR, 2010, RCR, "3dbucket", MINOR, TYPE_BUG_FIX, 8386 "fixed getting incorrect FDR curves (noted by D Glen)", 8387 NULL 8388 } , 8389 8390 { 16, MAR, 2010, RCR, "NIFTI", MICRO, TYPE_ENHANCE, 8391 "added NIFTI_ECODE_VOXBO for D. Kimberg", 8392 NULL 8393 } , 8394 8395 { 11, MAR, 2010, RCR, "3dsvm_common.c", MICRO, TYPE_GENERAL, 8396 "some compilers choke on mid-block variable definitions", 8397 NULL 8398 } , 8399 8400 { 9, MAR, 2010, RCR, "3dNotes", MICRO, TYPE_GENERAL, 8401 "send -help output to stdout, not stderr (req by T Nycum)", 8402 NULL 8403 } , 8404 8405 { 9, MAR, 2010, RCR, "thd_gifti.c", MICRO, TYPE_MODIFY, 8406 "init ptr and clear accidental debug output", 8407 NULL 8408 } , 8409 8410 { 8, MAR, 2010, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 8411 "modified option order in some help examples", 8412 NULL 8413 } , 8414 8415 { 8, MAR, 2010, RCR, "thd_gifti.c", MICRO, TYPE_MODIFY, 8416 "corresponding update of lt->index to lt->key", 8417 NULL 8418 } , 8419 8420 { 8, MAR, 2010, RCR, "GIFTI", MINOR, TYPE_MODIFY, 8421 "GIfTI LabelTable format change: Index to Key", 8422 "modified gifti_xml.[ch], gifti_io.[ch]" 8423 } , 8424 8425 { 5, MAR, 2010, RCR, "thd_gifti.c", MICRO, TYPE_MODIFY, 8426 "try to read gifti UINT32 as INT32 (for FreeSurfer aparc files)", 8427 NULL 8428 } , 8429 8430 { 4, MAR, 2010, RCR, "GIFTI", MINOR, TYPE_MODIFY, 8431 "minor changes (also see NITRC IDs 4619 and 4644)", 8432 " - for integers, make default approx test to be equality\n" 8433 " - small changes to zlib failure strings\n" 8434 " - cast to avoid compile warning on some systems\n" 8435 " - made NITRC gifti.dtd link that will not change" 8436 } , 8437 8438 { 3, MAR, 2010, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 8439 "when censoring, create uncensored ideals and sum", 8440 NULL 8441 } , 8442 8443 { 20, FEB, 2010, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 8444 "added -timing_to_1D, -tr and -min_frac for PPI scripting (and B Benson)", 8445 NULL 8446 } , 8447 8448 { 18, FEB, 2010, RCR, "SUMA_Makefile_NoDev", MICRO, TYPE_GENERAL, 8449 "added '--includedir /usr/local/netpbm' for libgts.a build on new Linux", 8450 NULL 8451 } , 8452 8453 { 5, FEB, 2010, RCR, "GIFTI", MINOR, TYPE_MODIFY, 8454 "thd_gifti: if LabelTable use INTENT_LABEL, suma_gifti.c: no normals", 8455 "done with Ziad" 8456 } , 8457 8458 { 21, JAN, 2010, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 8459 "added -tlrc_opts_at; made tiny mod to scaling operation", 8460 NULL 8461 } , 8462 8463 { 15, JAN, 2010, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 8464 "added -regress_fout yes/no option for G. Pagnoni", 8465 NULL 8466 } , 8467 8468 { 14, JAN, 2010, RCR, "3dVol2Surf", MINOR, TYPE_BUG_FIX, 8469 "Fixed crash w/labels on '-map_func seg_vals' -> NIML", 8470 "Problem found by Swaroop at Dartmouth." 8471 } , 8472 8473 { 12, JAN, 2010, RCR, "2dImReg", MICRO, TYPE_BUG_FIX, 8474 "Fixed crash if ny > nx. Go back to failure and ponder fix.", 8475 NULL 8476 } , 8477 8478 { 7, JAN, 2010, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 8479 "stdint.h should not be included on a SOLARIS_OLD system", 8480 NULL 8481 } , 8482 8483 { 6, JAN, 2010, RCR, "thd_intlist.c", MINOR, TYPE_BUG_FIX, 8484 "fixed sub-brick selection of datasets without labels (e.g. NIfTI)", 8485 NULL 8486 } , 8487 8488 { 24, DEC, 2009, RCR, "gifti_tool", MINOR, TYPE_NEW_OPT, 8489 "added -approx_gifti option", 8490 NULL 8491 } , 8492 8493 { 24, DEC, 2009, RCR, "GIFTI", MINOR, TYPE_ENHANCE, 8494 "added approximate difference functions", 8495 "- added gifti_approx_gifti_images, DA_pair, labeltables, diff_offset\n" 8496 "- added gifti_triangle_diff_offset\n" 8497 "- gifti_compare_coordsys takes comp_data param" 8498 } , 8499 8500 { 8, DEC, 2009, RCR, "GIFTI", MINOR, TYPE_ENHANCE, 8501 "added ability to read/write GIFTI LabelTables with colors in thd_gifti.c", 8502 NULL 8503 } , 8504 8505 { 4, DEC, 2009, RCR, "3dWarp", MICRO, TYPE_GENERAL, 8506 "add help example of going from +tlrc space to +orig space", 8507 NULL 8508 } , 8509 8510 { 30, NOV, 2009, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 8511 "afni crashes on short ANALYZE file from double fclose()", 8512 NULL 8513 } , 8514 8515 { 16, NOV, 2009, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 8516 "allow motion censoring with varying run lengths", 8517 "Also, if a max is applied in scaling, explicitly limit to [0,max].\n" 8518 } , 8519 8520 { 16, NOV, 2009, RCR, "1d_tool.py", MINOR, TYPE_ENHANCE, 8521 "allow motion censoring with varying run lengths", 8522 NULL 8523 } , 8524 8525 { 4, NOV, 2009, RCR, "Dimon", MICRO, TYPE_MODIFY, 8526 "small change to check on sort problems", 8527 NULL 8528 } , 8529 8530 { 27, OCT, 2009, RCR, "GIFTI", MINOR, TYPE_ENHANCE, 8531 "added support for optional LabelTable RGBA attributes", 8532 NULL 8533 } , 8534 8535 { 23, OCT, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 8536 "added -censor_fill and -censor_fill_par", 8537 "These options are to zero-pad TRs that were censored by 3dDeconvolve." 8538 } , 8539 8540 { 19, OCT, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8541 "added options for using 3dBlurInMask, instead of 3dmerge", 8542 "- added -blur_in_mask, -blur_in_automask and -blur_opts_BIM\n" 8543 "- added -sep_char and -subj_curly" 8544 } , 8545 8546 { 16, OCT, 2009, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 8547 "added -demean, to demean motion parameters, for example", 8548 "The polort 0 values should be more accurate baseline constants.\n" 8549 "Useful for creating a proper polort baseline w/3dSynthesize." 8550 } , 8551 8552 { 14, OCT, 2009, RCR, "3dTcat", MICRO, TYPE_ENHANCE, 8553 "allow creation of single volume dataset", 8554 "as requested by N Vack (among many others)" 8555 } , 8556 8557 { 6, OCT, 2009, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 8558 "added -set_run_lengths option, for varying run lengths", 8559 "Added for motion censoring and run padding." 8560 } , 8561 8562 { 2, OCT, 2009, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 8563 "also output cosines with -show_cormat_warnings", 8564 NULL 8565 } , 8566 8567 { 1, OCT, 2009, RCR, "@Reorder", MICRO, TYPE_MODIFY, 8568 "minor changes:", 8569 "- changed warnings on varying incidence counts (JB's woriding)\n" 8570 "- discard indices which are not valid sub-bricks\n" 8571 "- do not call 3dTstat if only one sub-brick" 8572 } , 8573 8574 { 1, OCT, 2009, RCR, "afni-general", MICRO, TYPE_GENERAL, 8575 "9/29, defined isblank() in case of SOLARIS_OLD ... and then removed it", 8576 NULL 8577 } , 8578 8579 { 29, SEP, 2009, RCR, "@Reorder", MINOR, TYPE_NEW_PROG, 8580 "script version of reorder plugin, for J. Bjork", 8581 NULL 8582 } , 8583 8584 { 16, SEP, 2009, RCR, "timing_tool.py", MICRO, TYPE_NEW_OPT, 8585 "added -scale_data for J Meltzer", 8586 NULL 8587 } , 8588 8589 { 16, SEP, 2009, RCR, "plug_vol2surf", MICRO, TYPE_ENHANCE, 8590 "can init debug level via AFNI_DEBUG_PLUG_VOL2SURF", 8591 NULL 8592 } , 8593 8594 { 16, SEP, 2009, RCR, "3ddot", MINOR, TYPE_BUG_FIX, 8595 "de-meaning data causes permission-based seg fault, apply means upon read", 8596 "Problem found by Giuseppe Pagnoni." 8597 } , 8598 8599 { 8, SEP, 2009, RCR, "realtime_receiver.py", MICRO, TYPE_MODIFY, 8600 "bind to open host, so a /etc/hosts entry is not required", 8601 NULL 8602 } , 8603 8604 { 4, SEP, 2009, RCR, "plug_realtime", MINOR, TYPE_ENHANCE, 8605 "registration can now be consistent across runs", 8606 "Reg Base can be 'Current': to set the base volume from the current run\n" 8607 "(call this the old way), 'Current & Keep': use current run, but then\n" 8608 "store that base and apply it to future runs, 'External Dataset': fix the\n" 8609 "base from some chosen dataset.\n" 8610 "\n" 8611 "Using 'Current & Keep' makes sense for realtime registration.\n" 8612 } , 8613 8614 { 4, SEP, 2009, RCR, "@update.afni.binaries", MICRO, TYPE_NEW_OPT, 8615 "if wget fails, try curl; added -curl and -testing options", 8616 NULL 8617 } , 8618 8619 { 28, AUG, 2009, RCR, "afni_util.py", MICRO, TYPE_BUG_FIX, 8620 "fixed make_CENSORTR_string, comma delimitation needs run: prefix", 8621 NULL 8622 } , 8623 8624 { 27, AUG, 2009, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 8625 "fixed motion_ prefix in '3dDeconvolve -censor'", 8626 "Problem found by B Bones." 8627 } , 8628 8629 { 27, AUG, 2009, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 8630 "added -regress_local_times, -regress_global_times", 8631 "Since the -local_times and -global_times options in 3dDeconvolve must be\n" 8632 "processed before the stimuli they refer to, it does nothing to pass them\n" 8633 "via -regress_opts_3dD. Hence, the options are needed.\n" 8634 } , 8635 8636 { 26, AUG, 2009, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 8637 "in scaling block, explicitly remove any negative data values", 8638 NULL 8639 } , 8640 8641 { 25, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_ENHANCE, 8642 "if volreg block, always create motion_${subj}_enorm.1D", 8643 NULL 8644 } , 8645 8646 { 25, AUG, 2009, RCR, "1d_tool.py", MICRO, TYPE_ENHANCE, 8647 "with -censor_motion, also output PREFIX_enorm.1D", 8648 NULL 8649 } , 8650 8651 { 21, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8652 "added -regress_censor_motion and -regress_censor_prev", 8653 "Motivated by L Thomas and B Bones." 8654 } , 8655 8656 { 21, AUG, 2009, RCR, "1d_tool.py", MICRO, TYPE_NEW_OPT, 8657 "added -show_censor_count", 8658 NULL 8659 } , 8660 8661 { 20, AUG, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 8662 "added motion censoring options", 8663 "Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask,\n" 8664 " -set_tr, -write_censor and -write_CENSORTR.\n" 8665 "Also modified afni_util.py, lib_afni1D.py and option_list.py." 8666 } , 8667 8668 { 14, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8669 "added -align_epi_ext_dset, to align anat to external EPI", 8670 "This may be important for multi-channel coil EPI data with low internal\n" 8671 "structural contrast. Users might align to the first (pre-steady-state)\n" 8672 "TR, even though that volume is not used in the analysis." 8673 } , 8674 8675 { 13, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8676 "added -volreg_tlrc_adwarp, to apply a manual Talairach transformation", 8677 NULL 8678 } , 8679 8680 { 10, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 8681 "truncate min dim to 3 sig bits for -volreg_tlrc_warp/-volreg_align_e2s", 8682 "The old default was 2 bits, -volreg_warp_dxyz overrides." 8683 } , 8684 8685 { 10, AUG, 2009, RCR, "3dSurf2Vol", MINOR, TYPE_ENHANCE, 8686 "allow processing of -overwrite and AFNI_DECONFLICT", 8687 NULL 8688 } , 8689 8690 { 6, AUG, 2009, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 8691 "fixed problems found by I Mukai and K Bahadur", 8692 "- fixed -volreg_align_to base as applied in align_epi_anat.py\n" 8693 "- fixed blur 'averages' computation when only one run" 8694 } , 8695 8696 { 4, AUG, 2009, RCR, "realtime_receiver.py", MINOR, TYPE_ENHANCE, 8697 "added basic demo interface and itemized exception traps", 8698 NULL 8699 } , 8700 8701 { 31, JUL, 2009, RCR, "prompt_user", MICRO, TYPE_ENHANCE, 8702 "apply some escape sequences, mostly to display newlines", 8703 NULL 8704 } , 8705 8706 { 29, JUL, 2009, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 8707 "fixed creation of extents mask when only 1 run", 8708 NULL 8709 } , 8710 8711 { 28, JUL, 2009, RCR, "3dREMLfit", MINOR, TYPE_MODIFY, 8712 "if known, require proper slice regressor ordering in -slibase* opts\n", 8713 NULL 8714 } , 8715 8716 { 27, JUL, 2009, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 8717 "use -slibase_sm instead of -slibase in 3dREMLfit", 8718 NULL 8719 } , 8720 8721 { 27, JUL, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 8722 "added -show_labels and -show_label_ordering", 8723 NULL 8724 } , 8725 8726 { 27, JUL, 2009, RCR, "3dREMLfit", MINOR, TYPE_NEW_OPT, 8727 "added -slibase_sm, for slice-major ordering of regressors", 8728 "RetroTS and afni_proc.py were incorrectly using this ordering.\n" 8729 "** Analysis done prior to this probably needs to be re-done." 8730 } , 8731 8732 { 27, JUL, 2009, RCR, "plug_realtime", MICRO, TYPE_ENHANCE, 8733 "added Y/N AFNI_REALTIME_reset_output_index, to start each dset at 001", 8734 "Also, changed prefix separator to double underscore '__'.", 8735 } , 8736 8737 { 27, JUL, 2009, RCR, "afni-general", MICRO, TYPE_GENERAL, 8738 "added SOLARIS_OLD atanhf #define to machdep.h", 8739 NULL 8740 } , 8741 8742 { 23, JUL, 2009, RCR, "afni_run_R", MINOR, TYPE_ENHANCE, 8743 "allow any number of args, but where first is program, last is output", 8744 NULL 8745 } , 8746 8747 { 23, JUL, 2009, RCR, "timing_tool.py", MINOR, TYPE_NEW_OPT, 8748 "added -partition option", 8749 NULL 8750 } , 8751 8752 { 22, JUL, 2009, RCR, "realtime_receiver.py", MAJOR, TYPE_NEW_PROG, 8753 "python replacement for serial helper", 8754 "New 'data_choice' options can be added to compute_data_for_serial_port\n" 8755 "for sending results of a different computation to the serial port." 8756 } , 8757 8758 { 16, JUL, 2009, RCR, "@update.afni.binaries", MICRO, TYPE_MODIFY, 8759 "check for 'wget' and whine to user if missing", 8760 NULL 8761 } , 8762 8763 { 14, JUL, 2009, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 8764 "added -max_rest, to limit the maximum duration of rest periods", 8765 NULL 8766 } , 8767 8768 { 7, JUL, 2009, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 8769 "warn users to modify script for _AM1 in case of basis function dmBLOCK", 8770 NULL 8771 } , 8772 8773 { 26, JUN, 2009, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 8774 "comment changes and mod to afni_util.py for line wrapping", 8775 NULL 8776 } , 8777 8778 { 25, JUN, 2009, RCR, "Dimon", MINOR, TYPE_BUG_FIX, 8779 "fixed dz sent to RT plugin for oblique datasets", 8780 NULL 8781 } , 8782 8783 { 25, JUN, 2009, RCR, "3dretroicor", MICRO, TYPE_BUG_FIX, 8784 "pass MRI_IMAGE structs without const", 8785 NULL 8786 } , 8787 8788 { 24, JUN, 2009, RCR, "afni-general", MINOR, TYPE_BUG_FIX, 8789 "applied print changes from B Feige (26 files):", 8790 "3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c\n" 8791 "suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c\n" 8792 "SUMA/ SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c\n" 8793 " SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c\n" 8794 " SUMA_ParseCommands.h SUMA_SphericalMapping.c\n" 8795 " SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c\n" 8796 " SUMA_compare_surfaces.c SUMA_xColBar.c\n" 8797 "svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c" 8798 } , 8799 8800 { 23, JUN, 2009, RCR, "NIFTI", MINOR, TYPE_BUG_FIX, 8801 "added 4 checks of alloc() returns", 8802 NULL 8803 } , 8804 8805 { 17, JUN, 2009, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 8806 "added -make_3dd_contrasts and used general accuracy in block durations", 8807 NULL 8808 } , 8809 8810 { 17, JUN, 2009, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 8811 "version 2.0 : call e2a alignment and warp to standard space ready", 8812 "- mask warped EPI by its extents (at volreg step)\n" 8813 "- added -volreg_no_extent_mask, to block this masking\n" 8814 "- added 'extents' to list of mask in -mask_apply\n" 8815 "- change block dividers to more visual '===' with block names" 8816 } , 8817 8818 { 15, JUN, 2009, RCR, "3dmerge", MINOR, TYPE_ENHANCE, 8819 "allowed short/byte datasets to use FIR blur, so no Fourier interpolation", 8820 "Also added Y/N AFNI_BLUR_INTS_AS_OLD env var to use previous method." 8821 } , 8822 8823 { 12, JUN, 2009, RCR, "xmat_tool.py", MICRO, TYPE_GENERAL, 8824 "used some wx IDs, per Daniel's suggestion", 8825 NULL 8826 } , 8827 8828 { 11, JUN, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8829 "added masking abilities", 8830 "- in mask block, try to create anat and group masks\n" 8831 "- added -mask_apply option, for choosing mask to apply to regression\n" 8832 "- added -align_opts_aea, for extra opts to align_epi_anat.py" 8833 } , 8834 8835 { 8, JUN, 2009, RCR, "afni_proc.py", MICRO, TYPE_NEW_OPT, 8836 "added -despike_mask, fixed missing block warning, reordered terminal opts", 8837 NULL 8838 } , 8839 8840 { 8, JUN, 2009, RCR, "afni_base.py", MICRO, TYPE_GENERAL, 8841 "added many afni_name descripts to __doc__ lines, check error in dset_dims", 8842 NULL 8843 } , 8844 8845 { 3, JUN, 2009, RCR, "3dcopy", MICRO, TYPE_MODIFY, 8846 "changed 'missing dataset' ERROR to 'missing view dataset' WARNING", 8847 NULL 8848 } , 8849 8850 { 29, MAY, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8851 "added -execute and now fail if block options have no corresponding blocks", 8852 NULL 8853 } , 8854 8855 { 29, MAY, 2009, RCR, "@build_afni_Xlib", MICRO, TYPE_MODIFY, 8856 "added -m64 if building for lib64 on a mac, fixed CFLAGS to allow a list", 8857 NULL 8858 } , 8859 8860 { 29, MAY, 2009, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 8861 "improved line wrapping", 8862 NULL 8863 } , 8864 8865 { 28, MAY, 2009, RCR, "strblast", MINOR, TYPE_BUG_FIX, 8866 "partial words had resulted in skipping ahead", 8867 "found by R Notestine of UCSD" 8868 } , 8869 8870 { 28, MAY, 2009, RCR, "afni_proc.py", MINOR, TYPE_GENERAL, 8871 "example updates for AFNI_data4 and new options", 8872 NULL 8873 } , 8874 8875 { 27, MAY, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8876 "updates for alignment/warp/varying run lengths", 8877 "- added -volreg_warp_dxyz option\n" 8878 "- if align a2e, add -no_ss to @auto_tlrc\n" 8879 "- for varying run lengths, fixed application of '-volreg_align_to last'\n" 8880 " and the -regress_est_blur_* options\n" 8881 " (blur estimation loops were modified for this)\n" 8882 "- warping to new grid truncates to 2 significant bits (if < 2 mm)" 8883 } , 8884 8885 { 21, MAY, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 8886 "added 'align' processing block and -volreg_align_e2a option", 8887 NULL 8888 } , 8889 8890 { 19, MAY, 2009, RCR, "3dbucket", MICRO, TYPE_GENERAL, 8891 "suggest -overwrite if -glueto is not allowed (for Mike B)", 8892 NULL 8893 } , 8894 8895 { 15, MAY, 2009, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 8896 "added -volreg_tlrc_warp option: can warp to standard space at volreg step", 8897 NULL 8898 } , 8899 8900 { 15, MAY, 2009, RCR, "afni_util", MICRO, TYPE_NEW_OPT, 8901 "added get_truncated_grid_dim", 8902 NULL 8903 } , 8904 8905 { 14, MAY, 2009, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 8906 "no 'rm rm.*' if such files were not created", 8907 NULL 8908 } , 8909 8910 { 14, MAY, 2009, RCR, "3dDeconvolve", MICRO, TYPE_BUG_FIX, 8911 "fixed -glt_label > -num_glt error message and -dmbase def for polort >= 0", 8912 NULL 8913 } , 8914 8915 { 12, MAY, 2009, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 8916 "fixed 'cat' of 'across-runs' ricor regressors", 8917 NULL 8918 } , 8919 8920 { 8, MAY, 2009, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 8921 "tlrc (for anat) is now a processing block, for easy manipulation", 8922 NULL 8923 } , 8924 8925 { 8, MAY, 2009, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 8926 "small cut-n-paste errors in db_mod.py and afni_util.py", 8927 NULL 8928 } , 8929 8930 { 5, MAY, 2009, RCR, "@update.afni.binaries", MINOR, TYPE_NEW_PROG, 8931 "another script to update the AFNI package", 8932 NULL 8933 } , 8934 8935 { 5, MAY, 2009, RCR, "plug_render", MINOR, TYPE_MODIFY, 8936 "now built from plug_null.c, so it will no longer be available", 8937 NULL 8938 } , 8939 8940 { 1, MAY, 2009, RCR, "Makefile.linux_xorg7_64", MICRO, TYPE_MODIFY, 8941 "link to local libGLws.a, as with 32-bit xorg7 package", 8942 NULL 8943 } , 8944 8945 { 30, APR, 2009, RCR, "3dcalc", MINOR, TYPE_MODIFY, 8946 "changed atan2(y,x) to proceed if y OR x is non-zero", 8947 NULL 8948 } , 8949 8950 { 30, APR, 2009, RCR, "thd_niftiread", MINOR, TYPE_MODIFY, 8951 "be sure to warn users when nifti is converted to float (w/dglen)", 8952 NULL 8953 } , 8954 8955 { 30, APR, 2009, RCR, "vol2surf", MINOR, TYPE_NEW_OPT, 8956 "return a node v2s time series when afni changes xhair position", 8957 NULL 8958 } , 8959 8960 { 29, APR, 2009, RCR, "to3d", MINOR, TYPE_BUG_FIX, 8961 "when opening -geomparent, allow for known non-afni extensions", 8962 NULL 8963 } , 8964 8965 { 29, APR, 2009, RCR, "vol2surf", MICRO, TYPE_MODIFY, 8966 "prep to return node v2s time series to suma, just check-in for now", 8967 "modified: afni.h, afni_niml.c, afni_vol2surf.c, vol2surf.c, vol2surf.h" 8968 } , 8969 8970 { 28, APR, 2009, RCR, "NIFTI", MINOR, TYPE_MODIFY, 8971 "uppercase file extensions are now valid", 8972 NULL 8973 } , 8974 8975 { 27, APR, 2009, RCR, "3dresample", MICRO, TYPE_MODIFY, 8976 "show help if no arguments", 8977 NULL 8978 } , 8979 8980 { 23, APR, 2009, RCR, "3dresample", MICRO, TYPE_MODIFY, 8981 "small changes to help", 8982 NULL 8983 } , 8984 8985 { 23, APR, 2009, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 8986 "moved function comments into the functions as docstrings", 8987 NULL 8988 } , 8989 8990 { 23, APR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 8991 "updates to help and tcsh options", 8992 "- added -f as a recommended tcsh option\n" 8993 "- added help section 'SCRIPT EXECUTION NOTE'\n" 8994 "- reordered help: intro, BLOCKS, DEFAULTS, EXAMPLES, NOTEs, OPTIONS\n" 8995 "- shifted execution command to separate line" 8996 } , 8997 8998 { 17, APR, 2009, RCR, "GIFTI", MICRO, TYPE_MODIFY, 8999 "more -set_extern_filelist help, allow DA size to vary over external files", 9000 NULL 9001 } , 9002 9003 { 14, APR, 2009, RCR, "afni_util.py", MICRO, TYPE_BUG_FIX, 9004 "possible to have truncation cause a negative variance in stdev_ub", 9005 NULL 9006 } , 9007 9008 { 14, APR, 2009, RCR, "NIFTI", MINOR, TYPE_NEW_OPT, 9009 "added sample nifticlib program: clib_01_read_write.c", 9010 NULL 9011 } , 9012 9013 { 11, APR, 2009, RCR, "afni-general", MICRO, TYPE_NEW_OPT, 9014 "added calls to opts.check_special_opts() in 7 more python programs:", 9015 "gen_epi_review.py, make_random_timing.py, make_stim_times.py\n" 9016 "neuro_deconvolve.py, python_module_test.py, timing_tool.py, ui_xmat.py" 9017 } , 9018 9019 { 11, APR, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9020 "added -volreg_regress_per_run", 9021 "This is to apply the motion parameters of each run as separate regressors." 9022 } , 9023 9024 { 11, APR, 2009, RCR, "option_list.py", MICRO, TYPE_NEW_OPT, 9025 "enhanced special option processing", 9026 "- added check_special_opts(), to be called before any processing\n" 9027 "- renamed -verbose_opts to -optlist_verbose\n" 9028 "- added -optlist_no_show_count" 9029 } , 9030 9031 { 11, APR, 2009, RCR, "eg_main_chrono.py", MICRO, TYPE_MODIFY, 9032 "removed -verbose opts (see -optlist_ options)", 9033 NULL 9034 } , 9035 9036 { 11, APR, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 9037 "added -derivative and -set_nruns, fixed -show_cormat_warnings typo", 9038 NULL 9039 } , 9040 9041 { 11, APR, 2009, RCR, "afni_proc.py", MICRO, TYPE_BUG_FIX, 9042 "fixed use of -regress_errts_prefix with blur est", 9043 NULL 9044 } , 9045 9046 { 10, APR, 2009, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 9047 "added -use_last_elem option for setting DICOM elements", 9048 NULL 9049 } , 9050 9051 { 10, APR, 2009, RCR, "to3d", MINOR, TYPE_NEW_OPT, 9052 "added -use_last_elem option for setting DICOM elements", 9053 "Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable." 9054 } , 9055 9056 { 10, APR, 2009, RCR, "1d_tool.py", MINOR, TYPE_MODIFY, 9057 "fix for old versions of python, like on solaris", 9058 "Each of copy.deepcopy(), sum(), and sort(reverse=True) failed." 9059 } , 9060 9061 { 9, APR, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 9062 "added -show_cormat_warnings and -cormat_cutoff", 9063 NULL 9064 } , 9065 9066 { 9, APR, 2009, RCR, "afni_proc.py", MAJOR, TYPE_NEW_OPT, 9067 "'official' release with RETROICOR processing block: ricor", 9068 "o added 'across-runs' ricor_regress_method\n" 9069 "o added ricor information and usage to help (see 'RETROICOR NOTE')\n" 9070 "o maintain unscaled shorts if they are input\n" 9071 "o added -ricor_datum" 9072 } , 9073 9074 { 8, APR, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 9075 "added -show_rows_cols option", 9076 NULL 9077 } , 9078 9079 { 2, APR, 2009, RCR, "3dDeconvolve", MINOR, TYPE_MODIFY, 9080 "changed CHECK_NIFTI to CHECK_NEEDS_FLOATS, including other dset types", 9081 NULL 9082 } , 9083 9084 { 1, APR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9085 "added 'ricor' processing block, for RETROICOR regressor removal", 9086 NULL 9087 } , 9088 9089 { 1, APR, 2009, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 9090 "slight change in add_line_wrapper()", 9091 NULL 9092 } , 9093 9094 { 31, MAR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9095 "small changes, and prep for retroicor", 9096 "- by default, the script will now terminate on any error\n" 9097 "- added -exit_on_error, -check_setup_errors\n" 9098 "- whine about block order problems" 9099 } , 9100 9101 { 31, MAR, 2009, RCR, "1d_tool.py", MINOR, TYPE_NEW_OPT, 9102 "added -pad_to_many_runs, -reverse", 9103 NULL 9104 } , 9105 9106 { 31, MAR, 2009, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 9107 "added get_typed_dset_attr_list, enhanced decode_1D_ints", 9108 NULL 9109 } , 9110 9111 { 31, MAR, 2009, RCR, "option_list.py", MICRO, TYPE_NEW_OPT, 9112 "added global -verbose_opts option", 9113 NULL 9114 } , 9115 9116 { 26, MAR, 2009, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 9117 "added helpstr to options", 9118 NULL 9119 } , 9120 9121 { 26, MAR, 2009, RCR, "1d_tool.py", MICRO, TYPE_BUG_FIX, 9122 "small array fix for older python in write()", 9123 NULL 9124 } , 9125 9126 { 26, MAR, 2009, RCR, "option_list.py", MICRO, TYPE_MODIFY, 9127 "base 'name' size on max len in show()", 9128 NULL 9129 } , 9130 9131 { 25, MAR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9132 "+view now comes from data: so it works with +tlrc", 9133 NULL 9134 } , 9135 9136 { 24, MAR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9137 "by default now, no mask is applied in the scale and regression steps", 9138 "Also added -regress_apply_mask option." 9139 } , 9140 9141 { 20, MAR, 2009, RCR, "@build_afni_Xlib", MINOR, TYPE_NEW_PROG, 9142 "moved from X/@build.Xlib, for distribution", 9143 "and added to SCRIPTS for building afni_src.tgz in Makefile.INCLUDE" 9144 } , 9145 9146 { 19, MAR, 2009, RCR, "1d_tool.py", MAJOR, TYPE_NEW_PROG, 9147 "added lib_afni1D.py and 1d_tool.py", 9148 "This is a library and tool for manipulating 1D files.\n" 9149 "Many functions will still be added." 9150 } , 9151 9152 { 19, MAR, 2009, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 9153 "a few additions and changes", 9154 "- allow container chars (e.g. []) in decode_1D_ints()\n" 9155 "- added is_valid_int_list()\n" 9156 "- changed str vars to istr (as str is a keyword)" 9157 } , 9158 9159 { 19, MAR, 2009, RCR, "eg_main_chrono.py", MINOR, TYPE_NEW_OPT, 9160 "added -verbose_opts option, for being verbose during option processing", 9161 NULL 9162 } , 9163 9164 { 18, MAR, 2009, RCR, "eg_main_chrono.py", MINOR, TYPE_NEW_PROG, 9165 "sample main python program using a library and chronological options", 9166 NULL 9167 } , 9168 9169 { 16, MAR, 2009, RCR, "3dBrickStat", MINOR, TYPE_BUG_FIX, 9170 "malloc extra val in case of percentile truncation", 9171 NULL 9172 } , 9173 9174 { 12, MAR, 2009, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9175 "warn user about masking in orig space", 9176 "- if despiking and no regression mask, apply -nomask\n" 9177 "- added 'MASKING NOTE', to suggest no regression mask until group space" 9178 } , 9179 9180 { 12, MAR, 2009, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9181 "added -regress_reml_exec and -regress_3dD_stop", 9182 "One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each." 9183 } , 9184 9185 { 10, MAR, 2009, RCR, "NIFTI", MICRO, TYPE_MODIFY, 9186 "added NIFTI_ECODEs 18-28 for the LONI MiND group", 9187 NULL 9188 } , 9189 9190 { 9, MAR, 2009, RCR, "3dcalc", MICRO, TYPE_MODIFY, 9191 "added edge/erode/dilate example to 3dcalc -help", 9192 NULL 9193 } , 9194 9195 { 9, MAR, 2009, RCR, "suma-general", MICRO, TYPE_MODIFY, 9196 "removed r_sprintf_long_to_hex from SUMA_Color.[ch]", 9197 NULL 9198 } , 9199 9200 { 9, MAR, 2009, RCR, "suma", MICRO, TYPE_NEW_OPT, 9201 "added -motif_ver option", 9202 NULL 9203 } , 9204 9205 { 6, MAR, 2009, RCR, "lesstif-general", MICRO, TYPE_MODIFY, 9206 "motif/lesstif : put AFNI_MOTIF_TYPE in Xm.h.in : see 'afni -motif_ver'", 9207 NULL 9208 } , 9209 9210 { 6, MAR, 2009, RCR, "3dDeconvolve", MINOR, TYPE_BUG_FIX, 9211 "if mri_automask_image() input is not really 3D, only apply clip", 9212 "3dD uses automask for misfit warning, let this apply to niml.dset" 9213 } , 9214 9215 { 5, MAR, 2009, RCR, "lesstif-general", MICRO, TYPE_MODIFY, 9216 "init for every assignable argument to XtVaGetValues (12 files)", 9217 NULL 9218 } , 9219 9220 { 5, MAR, 2009, RCR, "afni-general", MICRO, TYPE_MODIFY, 9221 "init for every assignable argument to XtVaGetValues (19 files)", 9222 NULL 9223 } , 9224 9225 { 5, MAR, 2009, RCR, "@build.Xlib", MICRO, TYPE_NEW_OPT, 9226 "change -noinstall option to -localinstall", 9227 NULL 9228 } , 9229 9230 { 5, MAR, 2009, RCR, "afni", MINOR, TYPE_BUG_FIX, 9231 "free vox_warp via KILL_list rather than directly when deleting dataset", 9232 "Fixes afni crash: set acpc markers -> acpc view -> orig view \n" 9233 " -> new markers -> acpc view -> death ..." 9234 } , 9235 9236 { 4, MAR, 2009, RCR, "@build.Xlib", MICRO, TYPE_NEW_OPT, 9237 "added -noinstall option", 9238 NULL 9239 } , 9240 9241 { 4, MAR, 2009, RCR, "afni", MICRO, TYPE_NEW_OPT, 9242 "added -motif_ver option", 9243 NULL 9244 } , 9245 9246 { 4, MAR, 2009, RCR, "X-general", MINOR, TYPE_MODIFY, 9247 "added openmotif build tree, updated @build.Xlib and README under X", 9248 NULL 9249 } , 9250 9251 { 3, MAR, 2009, RCR, "afni-general", MICRO, TYPE_MODIFY, 9252 "modified Makefile.linux_xorg7 and _64 for local X builds", 9253 NULL 9254 } , 9255 9256 { 3, MAR, 2009, RCR, "xutil.c", MICRO, TYPE_MODIFY, 9257 "another probably useless init (being cautious)", 9258 NULL 9259 } , 9260 9261 { 3, MAR, 2009, RCR, "@build.Xlib", MINOR, TYPE_NEW_PROG, 9262 "this is a build script for the local X packages", 9263 NULL 9264 } , 9265 9266 { 27, FEB, 2009, RCR, "X-general", MINOR, TYPE_MODIFY, 9267 "added lesstif and libXt trees to cvs", 9268 NULL 9269 } , 9270 9271 { 20, FEB, 2009, RCR, "afni-general", MICRO, TYPE_BUG_FIX, 9272 "many inits to appease lesstif and Xt (w/Ziad)", 9273 NULL 9274 } , 9275 9276 { 13, FEB, 2009, RCR, "dmat44.c", MICRO, TYPE_BUG_FIX, 9277 "cut-and-paste error ...", 9278 NULL 9279 } , 9280 9281 { 13, FEB, 2009, RCR, "afni-general", MICRO, TYPE_MODIFY, 9282 "malloc changes: 5 more files", 9283 "Friday the 13th, oooooooo... @ 18:31:30 EST: time will be 1234567890." 9284 } , 9285 9286 { 12, FEB, 2009, RCR, "afni-general", MICRO, TYPE_MODIFY, 9287 "added memsets following some malloc calls, or used calloc (14 files)", 9288 NULL 9289 } , 9290 9291 { 11, FEB, 2009, RCR, "3dDeconvolve", MICRO, TYPE_MODIFY, 9292 "removed duplicate -Rerrts option in output 3dREMLfit command", 9293 NULL 9294 } , 9295 9296 { 9, FEB, 2009, RCR, "xmat_tool.py", MINOR, TYPE_MODIFY, 9297 "random updates, plus those for Fedora 10", 9298 NULL 9299 } , 9300 9301 { 9, FEB, 2009, RCR, "python-general", MICRO, TYPE_GENERAL, 9302 "added new beginning-stage libraries lib_matplot.py and lib_wx.py", 9303 NULL 9304 } , 9305 9306 { 6, FEB, 2009, RCR, "NIFTI", MICRO, TYPE_MODIFY, 9307 "added NIFTI_ECODE_PYPICKLE for MH; imported HJ's cast changes", 9308 NULL 9309 } , 9310 9311 { 5, FEB, 2009, RCR, "make_random_timing.py", MICRO, TYPE_MODIFY, 9312 "added timing_tool.py use to sort times in example #7", 9313 NULL 9314 } , 9315 9316 { 4, FEB, 2009, RCR, "vol2surf", MINOR, TYPE_BUG_FIX, 9317 "fixed norm reversal application and norm dir check computation", 9318 "Thanks to Xiaopeng Zong for finding these problems." 9319 } , 9320 9321 { 4, FEB, 2009, RCR, "suma-general", MICRO, TYPE_MODIFY, 9322 "update SUMA_paperplane.c and Makefile.solaris28_gcc for v1280 builds", 9323 "Makefile now uses PREREQ=suma, gmake, -L/usr/dt/lib." 9324 } , 9325 9326 { 3, FEB, 2009, RCR, "afni-general", MICRO, TYPE_MODIFY, 9327 "fix machdep.h Makefile.solaris28_gcc for v1280 builds", 9328 NULL 9329 } , 9330 9331 { 7, JAN, 2009, RCR, "plug_crender", MICRO, TYPE_MODIFY, 9332 "if lesstif, set threshold slider bar width", 9333 NULL 9334 } , 9335 9336 { 2, JAN, 2009, RCR, "Makefile", MICRO, TYPE_MODIFY, 9337 "do not build balloon in Makefile.macosx_10.5_Intel_64 - libgsl is 32-bit", 9338 NULL 9339 } , 9340 9341 { 2, JAN, 2009, RCR, "afni_environ.c", MICRO, TYPE_BUG_FIX, 9342 "fixed bad lvalue when USE_TRACING is not defined", 9343 "also fixed define for USE_TRACING in solaris and cygwin Makefiles" 9344 } , 9345 9346 { 31, DEC, 2008, RCR, "afni", MINOR, TYPE_BUG_FIX, 9347 "fix for lesstif crash on 'where am i', along with ziad", 9348 NULL 9349 } , 9350 9351 { 24, DEC, 2008, RCR, "timing_tool.py", MICRO, TYPE_MODIFY, 9352 "redefine 'sum' for older python versions", 9353 "This also affects afni_util.py and make_random_timing.py." 9354 } , 9355 9356 { 15, DEC, 2008, RCR, "Makefile", MICRO, TYPE_MODIFY, 9357 "added USE_LESSTIF directive", 9358 "Modified Makefile.linux_xorg7[_64], Makefile.macosx_10.5_Intel[_64]." 9359 } , 9360 9361 { 10, DEC, 2008, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9362 "added new options for extra stimuli, RONI and an external volreg base", 9363 "- allow NIfTI datasets as input (but process as AFNI)\n" 9364 "- added -regress_extra_stim_files and -regress_extra_stim_labels\n" 9365 "- added -regress_RONI and -volreg_base_dset (for Jill Weisberg)" 9366 } , 9367 9368 { 8, DEC, 2008, RCR, "xmat_tool.py", MICRO, TYPE_MODIFY, 9369 "allow -test_libs to proceed without numpy", 9370 NULL 9371 } , 9372 9373 { 8, DEC, 2008, RCR, "Makefile", MICRO, TYPE_GENERAL, 9374 "added Makefile.macosx_10.5_G4", 9375 NULL 9376 } , 9377 9378 { 4, DEC, 2008, RCR, "Makefile.INCLUDE", MINOR, TYPE_MODIFY, 9379 "added balloon target for M Belmonte", 9380 "Also modified Makefile.linux_xorg7_64 and macosx_10.4_G5/Intel and 5_Int*." 9381 } , 9382 9383 { 4, DEC, 2008, RCR, "balloon", MICRO, TYPE_NEW_PROG, 9384 "new program by M Belmonte", 9385 NULL 9386 } , 9387 9388 { 1, DEC, 2008, RCR, "timing_tool.py", MAJOR, TYPE_NEW_PROG, 9389 "a tool for manipulating and evaluating stimulus timing files", 9390 "This is useful for getting statistics on rest timing." 9391 } , 9392 9393 { 1, DEC, 2008, RCR, "option_list.py", MICRO, TYPE_MODIFY, 9394 "added 'opt' param to more get_* functions", 9395 NULL 9396 } , 9397 9398 { 1, DEC, 2008, RCR, "make_random_timing.py", MICRO, TYPE_MODIFY, 9399 "moved min_mean_max_stdev to afni_util.py and modified help examples", 9400 NULL 9401 } , 9402 9403 { 24, NOV, 2008, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 9404 "added options -infile_list and -show_sorted_list", 9405 "The -show_sorted_list option will print a list of files by run/index." 9406 } , 9407 9408 { 21, NOV, 2008, RCR, "xmat_tool.py", MINOR, TYPE_NEW_OPT, 9409 "added Options menu, Show Cosmat and GUI help", 9410 "This is the initial release version, 1.0." 9411 } , 9412 9413 { 21, NOV, 2008, RCR, "xmat_tool.py", MINOR, TYPE_NEW_OPT, 9414 "added -test_libs option", 9415 NULL 9416 } , 9417 9418 { 21, NOV, 2008, RCR, "python_module_test.py", MINOR, TYPE_NEW_OPT, 9419 "removed 'R' from basic test list, and applied verb 2 to base usage", 9420 NULL 9421 } , 9422 9423 { 20, NOV, 2008, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 9424 "incorporated real-time volume writing from V. Roopchansingh of MCW", 9425 NULL 9426 } , 9427 9428 { 18, NOV, 2008, RCR, "xmat_tool.py", MINOR, TYPE_NEW_OPT, 9429 "added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff", 9430 "also added the main help" 9431 } , 9432 9433 { 18, NOV, 2008, RCR, "afni_xmat.py", MICRO, TYPE_MODIFY, 9434 "added extra_cols param to make_show_conds_str", 9435 NULL 9436 } , 9437 9438 { 7, NOV, 2008, RCR, "xmat_tool.py", MINOR, TYPE_MODIFY, 9439 "more updates:", 9440 "- scipy is only tested for when necessary\n" 9441 "- compute norms locally if no scipy\n" 9442 "- solve_against_1D, linear_combo: return error string instead of code\n" 9443 "- added -chrono option, to make all options chronological\n" 9444 " (so options are essentially scriptable)" 9445 } , 9446 9447 { 6, NOV, 2008, RCR, "xmat_tool.py", MINOR, TYPE_NEW_OPT, 9448 "pre-release updates:", 9449 " - added many initial command-line options\n" 9450 " - added plot_xmat_as_one toggle button\n" 9451 " - added computation of cosine matrix and cosmat_warnings\n" 9452 " - separated GUI code into new file gui_xmat.py" 9453 } , 9454 9455 { 6, NOV, 2008, RCR, "option_list.py", MICRO, TYPE_NEW_OPT, 9456 "added opt param to get_type_opt and get_type_list", 9457 "had to modify calls in make_random_timing.py and gen_epi_review.py" 9458 } , 9459 9460 { 6, NOV, 2008, RCR, "python_module_test.py", MINOR, TYPE_NEW_OPT, 9461 "added option -full_test", 9462 NULL 9463 } , 9464 9465 { 4, NOV, 2008, RCR, "plug_vol2surf", MICRO, TYPE_MODIFY, 9466 "fail if NIML output dataset does end in .niml.dset", 9467 NULL 9468 } , 9469 9470 { 4, NOV, 2008, RCR, "3dVol2Surf", MICRO, TYPE_MODIFY, 9471 "fail if NIML output dataset does end in .niml.dset", 9472 NULL 9473 } , 9474 9475 { 4, NOV, 2008, RCR, "vol2surf", MICRO, TYPE_MODIFY, 9476 "only complain about statsym_string in debug mode", 9477 NULL 9478 } , 9479 9480 { 31, OCT, 2008, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 9481 "moved functions encode_1D_ints and decode_1D_ints here", 9482 NULL 9483 } , 9484 9485 { 31, OCT, 2008, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 9486 "added -show_timing_stats option", 9487 "Also, made a small change affecting timing (old results will not match)." 9488 } , 9489 9490 { 29, OCT, 2008, RCR, "xmat_tool.py", MINOR, TYPE_MODIFY, 9491 "if the X-matrix has a constant regressor, do not de-mean it", 9492 "In such a case, the cormat would not exactly be a correlation matrix." 9493 } , 9494 9495 { 29, OCT, 2008, RCR, "python_module_test.py", MINOR, TYPE_NEW_PROG, 9496 "program to test python module imports (interface to module_test_lib.py)", 9497 NULL 9498 } , 9499 9500 { 28, OCT, 2008, RCR, "module_test_lib.py", MINOR, TYPE_NEW_PROG, 9501 "library to test python module imports", 9502 "One might want to apply this module at the top of any python file." 9503 } , 9504 9505 { 28, OCT, 2008, RCR, "xmat_tool.py", MICRO, TYPE_MODIFY, 9506 "use module_test_lib to test imports", 9507 NULL 9508 } , 9509 9510 { 27, OCT, 2008, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9511 "added -regress_motion_file option", 9512 NULL 9513 } , 9514 9515 { 27, OCT, 2008, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 9516 "added -offset option", 9517 NULL 9518 } , 9519 9520 { 27, OCT, 2008, RCR, "make_random_timing.py", MINOR, TYPE_BUG_FIX, 9521 "actually applied -min_rest, sorry...", 9522 NULL 9523 } , 9524 9525 { 24, OCT, 2008, RCR, "xmat_tool.py", SUPER, TYPE_NEW_PROG, 9526 "program to inspect a .xmat.1D X-matrix, possibly against a time series", 9527 "This is a Graphical tool for plotting a design matrix, reviewing\n" 9528 "condition numbers or the correlation matrix, and fitting to a 1D\n" 9529 "time series." 9530 } , 9531 9532 { 23, OCT, 2008, RCR, "Makefile.INCLUDE", MINOR, TYPE_BUG_FIX, 9533 "removed reference to cdflib, for 'make afni_src.tgz'", 9534 NULL 9535 } , 9536 9537 { 23, OCT, 2008, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 9538 "added lists_are_same function", 9539 NULL 9540 } , 9541 9542 { 20, OCT, 2008, RCR, "afni_util.py", MINOR, TYPE_NEW_OPT, 9543 "added write_text_to_file function", 9544 NULL 9545 } , 9546 9547 { 20, OCT, 2008, RCR, "afni_driver.c", MINOR, TYPE_NEW_OPT, 9548 "added 'GETENV' to the list of DRIVE_AFNI commands", 9549 NULL 9550 } , 9551 9552 { 16, OCT, 2008, RCR, "thd_mastery", MICRO, TYPE_MODIFY, 9553 "THD_copy_dset_subs should not need to add a warp structure", 9554 NULL 9555 } , 9556 9557 { 14, OCT, 2008, RCR, "thd_mastery", MICRO, TYPE_MODIFY, 9558 "verify sub-brick list in THD_copy_dset_subs()", 9559 NULL 9560 } , 9561 9562 { 14, OCT, 2008, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 9563 "added wrap string param to add_line_wrappers (to wrap with newlines)", 9564 NULL 9565 } , 9566 9567 { 8, OCT, 2008, RCR, "NIFTI", MICRO, TYPE_MODIFY, 9568 "allow cbl with indices in 0..nt*nu*nv*nw-1", 9569 NULL 9570 } , 9571 9572 { 7, OCT, 2008, RCR, "NIFTI", MICRO, TYPE_MODIFY, 9573 "added nifti_NBL_matches_nim() check for write_bricks()", 9574 NULL 9575 } , 9576 9577 { 2, OCT, 2008, RCR, "GIFTI", MICRO, TYPE_MODIFY, 9578 "minor changes", 9579 "- separate diffs in DAs from those in gifti_image\n" 9580 "- decode additional data types: INT8, UINT16, INT64\n" 9581 "- add link flags to libgiftiio_la target" 9582 } , 9583 9584 { 29, SEP, 2008, RCR, "3dmatmult", MAJOR, TYPE_NEW_PROG, 9585 "program to multiply AFNI datasets slice-by-slice as matrices", 9586 NULL 9587 } , 9588 9589 { 23, SEP, 2008, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9590 "added -remove_preproc_files option (akin to -move_preproc_files)", 9591 NULL 9592 } , 9593 9594 { 23, SEP, 2008, RCR, "gen_epi_review.py", MINOR, TYPE_MODIFY, 9595 "in script, check for existence of given datasets\n", 9596 NULL 9597 } , 9598 9599 { 17, SEP, 2008, RCR, "make_stim_times.py", MINOR, TYPE_NEW_OPT, 9600 "added -labels option, for including labels in filenames", 9601 NULL 9602 } , 9603 9604 { 16, SEP, 2008, RCR, "3drefit", MINOR, TYPE_BUG_FIX, 9605 "allow attribute editing of NIfTI datasets", 9606 NULL 9607 } , 9608 9609 { 10, SEP, 2008, RCR, "plug_realtime", MICRO, TYPE_BUG_FIX, 9610 "re-added sending of magic_bye string on MP socket close", 9611 NULL 9612 } , 9613 9614 { 3, SEP, 2008, RCR, "plug_realtime", MICRO, TYPE_MODIFY, 9615 "moved drive_wait execution to RT_tell_afni", 9616 NULL 9617 } , 9618 9619 { 2, SEP, 2008, RCR, "GIFTI", MICRO, TYPE_MODIFY, 9620 "have distribution Makefiles build with GIFTI/expat/zlib", 9621 NULL 9622 } , 9623 9624 { 29, AUG, 2008, RCR, "vol2surf", MINOR, TYPE_MODIFY, 9625 "fill in COLMS_STATSYM attribute when writing .niml.dset dataset", 9626 NULL 9627 } , 9628 9629 { 26, AUG, 2008, RCR, "3dAllineate", MINOR, TYPE_BUG_FIX, 9630 "initialized ntask in all cases", 9631 NULL 9632 } , 9633 9634 { 22, AUG, 2008, RCR, "Dimon", MICRO, TYPE_NEW_OPT, 9635 "added -drive_wait option", 9636 NULL 9637 } , 9638 9639 { 22, AUG, 2008, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 9640 "added DRIVE_WAIT command string", 9641 "The command will be executed after the first volume is processed,\n" 9642 "which is good for opening windows appropriate to a new dataset." 9643 } , 9644 9645 { 21, AUG, 2008, RCR, "afni", MINOR, TYPE_NEW_OPT, 9646 "added -disable_done option to safeguard real-time mode", 9647 NULL 9648 } , 9649 9650 { 21, AUG, 2008, RCR, "Dimon", MICRO, TYPE_MODIFY, 9651 "updated help and suggest -num_slices with -sleep_init", 9652 NULL 9653 } , 9654 9655 { 21, AUG, 2008, RCR, "afni-general", MINOR, TYPE_MODIFY, 9656 "in edt_dsetitems, if storage mode can be inferred from prefix, apply it", 9657 NULL 9658 } , 9659 9660 { 21, AUG, 2008, RCR, "ANOVA", MINOR, TYPE_MODIFY, 9661 "use DSET_BRIKNAME for dataset control, as that is updated for smode", 9662 NULL 9663 } , 9664 9665 { 18, AUG, 2008, RCR, "plug_realtime", MINOR, TYPE_MODIFY, 9666 "increase DRIVE_LIMIT to 4Kb, read env vars each run", 9667 "These variables can now be controlled through drive_afni 'SETENV'\n" 9668 "(either via 'plugout_drive' or 'Dimon -drive_afni'):\n" 9669 " - AFNI_REALTIME_Mask_Vals : specify what gets sent to serial_helper\n" 9670 " - AFNI_REALTIME_SHOW_TIMES : specify whether to show data timestamps\n" 9671 " - AFNI_REALTIME_SEND_VER : specify whether to send comm version" 9672 } , 9673 9674 { 15, AUG, 2008, RCR, "afni", MINOR, TYPE_BUG_FIX, 9675 "init graph->grid_spacing, to prevent potential div by 0 via DRIVE", 9676 NULL 9677 } , 9678 9679 { 14, AUG, 2008, RCR, "Dimon", MICRO, TYPE_MODIFY, 9680 "moved num_slices check to separate function", 9681 NULL 9682 } , 9683 9684 { 14, AUG, 2008, RCR, "3dBrickStat", MINOR, TYPE_BUG_FIX, 9685 "do not automatically print -max along with -var", 9686 NULL 9687 } , 9688 9689 { 5, AUG, 2008, RCR, "to3d", MINOR, TYPE_BUG_FIX, 9690 "re-added the un16 fix from July 1", 9691 NULL 9692 } , 9693 9694 { 3, AUG, 2008, RCR, "nifti_tool", MINOR, TYPE_NEW_OPT, 9695 "added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old", 9696 NULL 9697 } , 9698 9699 { 3, AUG, 2008, RCR, "nifticlib", MINOR, TYPE_MODIFY, 9700 "added swap ability for ANALYZE 7.5 format, and made swapping complete", 9701 "- added nifti_analyze75 struct\n" 9702 "- modified swap_nifti_header to swap all fields (analyze or nifti)\n" 9703 "- added regression testing script c16.rand.swap\n" 9704 "These changes were motivated by C Burns." 9705 } , 9706 9707 { 31, JUL, 2008, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 9708 "added -num_slices option, and full real-time example E", 9709 NULL 9710 } , 9711 9712 { 31, JUL, 2008, RCR, "serial_helper", MINOR, TYPE_NEW_OPT, 9713 "added HELLO version 2 to work as -disp_all", 9714 "See 'HELLO versions' from 'serial_helper -help' for details.\n" 9715 "See 'example E' from 'Dimon -help' for a complete testing example." 9716 } , 9717 9718 { 31, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 9719 "enhancements to communication with serial helper", 9720 "- added 'Motion Only' to methods\n" 9721 "- parameter methods can easily be switched per run\n" 9722 "- SEND_VER replaces HELLO_VER as Y/N variable\n" 9723 } , 9724 9725 { 30, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 9726 "added HELLO version 1 and show_times option", 9727 "These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES." 9728 } , 9729 9730 { 30, JUL, 2008, RCR, "serial_helper", MINOR, TYPE_NEW_OPT, 9731 "added HELLO version 1 and -show_times option", 9732 NULL 9733 } , 9734 9735 { 29, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_MODIFY, 9736 "print more socket error info, send MP vals w/out mask", 9737 NULL 9738 } , 9739 9740 { 29, JUL, 2008, RCR, "serial_helper", MINOR, TYPE_MODIFY, 9741 "captured and output more signal and error info, flushed output buffer", 9742 NULL 9743 } , 9744 9745 { 28, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_BUG_FIX, 9746 "alter check for bad socket: use tcp_alivecheck over tcp_writecheck", 9747 NULL 9748 } , 9749 9750 { 25, JUL, 2008, RCR, "Dimon", MINOR, TYPE_MODIFY, 9751 "allow -sleep_vol to be very small without early run termination", 9752 NULL 9753 } , 9754 9755 { 23, JUL, 2008, RCR, "3dttest", MINOR, TYPE_NEW_OPT, 9756 "added -base1_dset option, where -base1 value can vary over voxels\n", 9757 "Added for M Beauchamp." 9758 } , 9759 9760 { 18, JUL, 2008, RCR, "3dNLfim", MINOR, TYPE_MODIFY, 9761 "listed signal and noise models in -help output", 9762 NULL 9763 } , 9764 9765 { 17, JUL, 2008, RCR, "3dNLfim", MINOR, TYPE_MODIFY, 9766 "warn the user if DSET_NVALS is not the same as DSET_NUMTIMES", 9767 "That would suggest the dataset has no time axis." 9768 } , 9769 9770 { 16, JUL, 2008, RCR, "serial_helper", MINOR, TYPE_NEW_OPT, 9771 "added -disp_all to give formatted display of 'all' mask data", 9772 "This was added for P Kundu.\n" 9773 } , 9774 9775 { 16, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_NEW_OPT, 9776 "added choice of 'Vals to Send' to serial_helper", 9777 "Can now send index,i,j,k,x,y,z,value for every value in mask." 9778 } , 9779 9780 { 14, JUL, 2008, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 9781 "added -sleep_init, -sleep_vol, -sleep_frac", 9782 "These options control the timeout periods between data checks." 9783 } , 9784 9785 { 14, JUL, 2008, RCR, "plug_realtime", MINOR, TYPE_MODIFY, 9786 "terminate TCP transmission to serial_helper if mask is bad\n", 9787 NULL 9788 } , 9789 9790 { 14, JUL, 2008, RCR, "afni_history", MINOR, TYPE_MODIFY, 9791 "a single integer option is interpreted as with -past_entries", 9792 NULL 9793 } , 9794 9795 { 11, JUL, 2008, RCR, "Dimon", MICRO, TYPE_MODIFY, 9796 "include last 4 elements of obl_matrix, even though probably useless", 9797 NULL 9798 } , 9799 9800 { 10, JUL, 2008, RCR, "plug_realtime", MAJOR, TYPE_MODIFY, 9801 "receive oblique transform matrix via new OBLIQUE_XFORM interface", 9802 NULL 9803 } , 9804 9805 { 10, JUL, 2008, RCR, "Dimon", MAJOR, TYPE_MODIFY, 9806 "if the data is oblique, pass the transformation matrix to plug_realtime", 9807 NULL 9808 } , 9809 9810 { 9, JUL, 2008, RCR, "plug_realtime", MICRO, TYPE_MODIFY, 9811 "if user closes graph window, allow comm with serial_helper to proceed", 9812 NULL 9813 } , 9814 9815 { 7, JUL, 2008, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 9816 "move extra newline from args_as_command to show_args_as_command", 9817 NULL 9818 } , 9819 9820 { 3, JUL, 2008, RCR, "plug_drawdset", MICRO, TYPE_BUG_FIX, 9821 "edt_dset_items.c: for .hdr, use .img brick file, storage_mode = BY_NIFTI", 9822 NULL 9823 } , 9824 9825 { 2, JUL, 2008, RCR, "Dimon", MICRO, TYPE_MODIFY, 9826 "provide suggestions in the case of a real-time TCP connection failure", 9827 NULL 9828 } , 9829 9830 { 1, JUL, 2008, RCR, "to3d", MINOR, TYPE_BUG_FIX, 9831 "fixed crash in case of mosaic and un16, no longer having im data", 9832 "Problem found by R. McColl." 9833 } , 9834 9835 { 1, JUL, 2008, RCR, "Makefile.INCLUDE", MINOR, TYPE_MODIFY, 9836 "modified the make system for building programs in the install directory", 9837 "- modified Makefile.INCLUDE's INFLAGS and ISFLAGS\n" 9838 "- modified SUMA_INPATH in SUMA_Makefile_NoDev.\n" 9839 "- removed 'rickr/' dirs from includes in mrilib.h, plug_crender.c and\n" 9840 " 3dAllineate.c\n\n" 9841 "Requested by V. Roopchansingh of MCW.\n" 9842 } , 9843 9844 { 30, JUN, 2008, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 9845 "added -gen_epi_review and -no_epi_review options", 9846 "By default, a drive_afni script to review EPI data is now generated." 9847 } , 9848 9849 { 30, JUN, 2008, RCR, "gen_epi_review.py", MINOR, TYPE_MODIFY, 9850 "make script executable, decrease sleep, add usage comment in script", 9851 NULL 9852 } , 9853 9854 { 27, JUN, 2008, RCR, "gen_epi_review.py", MAJOR, TYPE_NEW_PROG, 9855 "generate afni/drive_afni script to review initial EPI data", 9856 "This program was written to be called from the afni_proc.py output script." 9857 } , 9858 9859 { 27, JUN, 2008, RCR, "afni_util.py", MICRO, TYPE_MODIFY, 9860 "small modification to find_command_end", 9861 NULL 9862 } , 9863 9864 { 25, JUN, 2008, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 9865 "added -past_entries option", 9866 NULL 9867 } , 9868 9869 { 25, JUN, 2008, RCR, "howto", MINOR, TYPE_MODIFY, 9870 "put disclaimers at the tops of HowTo #1, #2, and #5", 9871 "references to current AFNI class handouts were included" 9872 } , 9873 9874 { 24, JUN, 2008, RCR, "3dDeconvolve", MINOR, TYPE_MODIFY, 9875 "added the ability to output 1D iresp datasets", 9876 NULL 9877 } , 9878 9879 { 20, JUN, 2008, RCR, "libmri", MINOR, TYPE_MODIFY, 9880 "thd_niftiread: do not scale to float if scale=1 and inter=0", 9881 NULL 9882 } , 9883 9884 { 19, JUN, 2008, RCR, "file_tool", MICRO, TYPE_MODIFY, 9885 "removed printing of pointers in disp_ functions", 9886 NULL 9887 } , 9888 9889 { 19, JUN, 2008, RCR, "make_stim_times.py", MINOR, TYPE_MODIFY, 9890 "help update, added -show_valid_opts, use '*' as separator w/amplitudes", 9891 NULL 9892 } , 9893 9894 { 16, JUN, 2008, RCR, "file_tool", MINOR, TYPE_MODIFY, 9895 "show output for multiple bad files when using -show_bad_backslash", 9896 NULL 9897 } , 9898 9899 { 13, JUN, 2008, RCR, "3dclust", MINOR, TYPE_MODIFY, 9900 "in the help, Volume defaults to microliters, unless -dxyz=1 is used", 9901 NULL 9902 } , 9903 9904 { 13, JUN, 2008, RCR, "nifti_tool", MINOR, TYPE_NEW_OPT, 9905 "added -with_zlib, and ability to add extensions via 'file:FILENAME'", 9906 "extension update added for J. Gunter" 9907 } , 9908 9909 { 13, JUN, 2008, RCR, "nifticlib", MINOR, TYPE_NEW_OPT, 9910 "added nifti_compiled_with_zlib()", 9911 NULL 9912 } , 9913 9914 { 12, JUN, 2008, RCR, "neuro_deconvolve.py", MINOR, TYPE_NEW_PROG, 9915 "generate 3dTfitter script to deconvolve a BOLD signal into a neuro signal", 9916 NULL 9917 } , 9918 9919 { 12, JUN, 2008, RCR, "afni_util.py", MICRO, TYPE_NEW_OPT, 9920 "added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D", 9921 "also, updated find_last_space to deal with long strings" 9922 } , 9923 9924 { 12, JUN, 2008, RCR, "afni_proc.py", MICRO, TYPE_MODIFY, 9925 "shifted code to afni_util.get_dset_reps_tr and .get_default_polort", 9926 NULL 9927 } , 9928 9929 { 6, JUN, 2008, RCR, "plug_crender", MINOR, TYPE_BUG_FIX, 9930 "integral threshold was off by 1", 9931 NULL 9932 } , 9933 9934 { 6, JUN, 2008, RCR, "make_random_timing.py", MICRO, TYPE_MODIFY, 9935 "get_*_opt now returns an error code", 9936 NULL 9937 } , 9938 9939 { 2, JUN, 2008, RCR, "GIFTI", MICRO, TYPE_GENERAL, 9940 "added CMakeLists.txt and XMLCALL update from Simon Warfield", 9941 "also added LICENSE.gifti" 9942 } , 9943 9944 { 2, JUN, 2008, RCR, "model_demri_3", MICRO, TYPE_MODIFY, 9945 "small help update to clarify residual C curve input", 9946 NULL 9947 } , 9948 9949 { 29, MAY, 2008, RCR, "model_demri_3", MICRO, TYPE_BUG_FIX, 9950 "help update to clarify use of AFNI_MODEL_D3_R1I_DSET", 9951 NULL 9952 } , 9953 9954 { 22, MAY, 2008, RCR, "3dTshift", MINOR, TYPE_BUG_FIX, 9955 "with -rlt, slices without any time shift must still be processed", 9956 "problem noticed by Jie Huang" 9957 } , 9958 9959 { 21, MAY, 2008, RCR, "model_demri_3", MINOR, TYPE_BUG_FIX, 9960 "fixed incorrect scaling in Cp computation", 9961 "The error was introduced on April 8, 2008." 9962 } , 9963 9964 { 21, MAY, 2008, RCR, "make_stim_times.py", MICRO, TYPE_NEW_OPT, 9965 "added -amplitudes option (for Rutvik Desai)", 9966 NULL 9967 } , 9968 9969 { 18, MAY, 2008, RCR, "make_random_timing.py", MINOR, TYPE_NEW_OPT, 9970 "added options for TR-locking and storing '3dDeconvolve -nodata' examples", 9971 "- added shuffle() to replace that from random (cannot produce all perms)\n" 9972 "- added options -tr, -tr_locked and -save_3dd_cmd\n" 9973 "- changed -stim_time option to -stim_dur" 9974 } , 9975 9976 { 18, MAY, 2008, RCR, "afni_history", MICRO, TYPE_MODIFY, 9977 "sped up comparison (since histories have gotten long)", 9978 NULL 9979 } , 9980 9981 { 17, MAY, 2008, RCR, "afni_proc.py", MINOR, TYPE_MODIFY, 9982 "check result of 3dDeconvolve execution in output script", 9983 "If 3dDeconvolve fails, terminate the script so that the user can\n" 9984 "see what happened." 9985 } , 9986 9987 { 14, MAY, 2008, RCR, "model_demri_3", MINOR, TYPE_BUG_FIX, 9988 "fixed application of decay term", 9989 NULL 9990 } , 9991 9992 { 13, MAY, 2008, RCR, "GIFTI", MINOR, TYPE_NEW_OPT, 9993 "gifticlib-1.0.0: initial release", 9994 "includes support for (set/clear/read/write) external data files" 9995 } , 9996 9997 { 13, MAY, 2008, RCR, "gifti_tool", MINOR, TYPE_NEW_OPT, 9998 "added -set_extern_filelist option, and help for using external data files", 9999 NULL 10000 } , 10001 10002 { 9, MAY, 2008, RCR, "GIFTI", MINOR, TYPE_MODIFY, 10003 "gifticlib-0.0.18: giiCoordSystem is now an array of struct pointers", 10004 "modified GIFTI library, along with suma_gifti.c" 10005 } , 10006 10007 { 8, MAY, 2008, RCR, "model_demri_3", MINOR, TYPE_MODIFY, 10008 "updated help, NFIRST does not need to imply injection time", 10009 NULL 10010 } , 10011 10012 { 7, MAY, 2008, RCR, "option_list.py", MINOR, TYPE_NEW_OPT, 10013 "added get_type_list and other accessor functions", 10014 NULL 10015 } , 10016 10017 { 7, MAY, 2008, RCR, "plug_3Ddump_V2", MINOR, TYPE_BUG_FIX, 10018 "allow 4D datasets to be opened (so that buckets are again usable)", 10019 "PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES..." 10020 } , 10021 10022 { 7, MAY, 2008, RCR, "make_random_timing.py", MAJOR, TYPE_NEW_PROG, 10023 "generate random stimulus timing files", 10024 "This generates random timing files suitable for use in 3dDeconvolve.\n" 10025 "The timing is not restricted to a TR grid, though that is possible.\n" 10026 "Consider use with '3dDeconvolve -nodata'." 10027 } , 10028 10029 { 1, MAY, 2008, RCR, "model_demri_3", MINOR, TYPE_BUG_FIX, 10030 "treat RESID_CT as Ct(t), not C(t)", 10031 NULL 10032 } , 10033 10034 { 30, APR, 2008, RCR, "make_stim_times.py", MICRO, TYPE_BUG_FIX, 10035 "replaced make_stim_files with make_stim_times.py in help", 10036 NULL 10037 } , 10038 10039 { 10, APR, 2008, RCR, "afni_proc.py", MICRO, TYPE_GENERAL, 10040 "updated the -help with information regarding runs of different lengths", 10041 NULL 10042 } , 10043 10044 { 8, APR, 2008, RCR, "2dImReg", MINOR, TYPE_BUG_FIX, 10045 "allow zero slices, passing input as result", 10046 "Choleski factorization would fail on an empty slice. In this case,\n" 10047 "return the input slices as the result (instead of crashing).\n" 10048 "Done with D Glen." 10049 } , 10050 10051 { 8, APR, 2008, RCR, "3dNLfim", MICRO, TYPE_MODIFY, 10052 "only update output every 100 voxels", 10053 NULL 10054 } , 10055 10056 { 8, APR, 2008, RCR, "model_demri_3", MINOR, TYPE_NEW_ENV, 10057 "allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset", 10058 "e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig" 10059 } , 10060 10061 { 2, APR, 2008, RCR, "ANOVA", MINOR, TYPE_MODIFY, 10062 "extended maximum number of contrasts to 75", 10063 NULL 10064 } , 10065 10066 { 1, APR, 2008, RCR, "ANOVA", MINOR, TYPE_MODIFY, 10067 "increased internal memory for 3dbucket and 3drefit command creation", 10068 NULL 10069 } , 10070 10071 { 31, MAR, 2008, RCR, "ANOVA", MINOR, TYPE_MODIFY, 10072 "extended maximum number of means, diffs and contrasts to 50", 10073 NULL 10074 } , 10075 10076 { 28, MAR, 2008, RCR, "gifticlib", MICRO, TYPE_NEW_OPT, 10077 "added routines to copy MetaData", 10078 NULL 10079 } , 10080 10081 { 28, MAR, 2008, RCR, "gifti_tool", MINOR, TYPE_NEW_OPT, 10082 "added -copy_gifti_meta and -copy_DA_meta options", 10083 NULL 10084 } , 10085 10086 { 26, MAR, 2008, RCR, "gifticlib", MICRO, TYPE_MODIFY, 10087 "in compare, if comp_data is not set, state the fact", 10088 NULL 10089 } , 10090 10091 { 25, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_MODIFY, 10092 "minor changes:", 10093 " - NIFTI_INTENT_NONE is considered valid\n" 10094 " - added compare_gifti_data functions\n" 10095 " - LabelTables are now written using CDATA" 10096 } , 10097 10098 { 25, MAR, 2008, RCR, "gifti_tool", MINOR, TYPE_MODIFY, 10099 "the -compare_data option is not separate from -compare_gifti", 10100 NULL 10101 } , 10102 10103 { 24, MAR, 2008, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 10104 "added GERT_Reco options (request of D Glen)", 10105 " -gert_filename : specify a name for the GERT_Reco script\n" 10106 " -gert_nz : override nz=1 in mosaic image files\n" 10107 " -gert_to3d_prefix : specify a dataset prefix for the to3d command" 10108 } , 10109 10110 { 24, MAR, 2008, RCR, "@Align_Centers", MINOR, TYPE_BUG_FIX, 10111 "applied proper follower dataset orientation and floating point shifts", 10112 "The shift applied to the child datasets was based on the parent's\n" 10113 "orientation. The shifts were also being truncated to integers.\n" 10114 "Changed with D Glen.\n" 10115 } , 10116 10117 { 18, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_NEW_OPT, 10118 "added comparison functions to gifticlib", 10119 NULL 10120 } , 10121 10122 { 20, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_NEW_ENV, 10123 "AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix", 10124 "For example, setting this to YES will allow writing surface data to NIfTI." 10125 } , 10126 10127 { 18, MAR, 2008, RCR, "gifti_tool", MINOR, TYPE_NEW_OPT, 10128 "added -compare_gifti option", 10129 "See 'gifti_tool -help' for details, including example #7." 10130 } , 10131 10132 { 17, MAR, 2008, RCR, "Dimon", MINOR, TYPE_MODIFY, 10133 "if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d", 10134 NULL 10135 } , 10136 10137 { 13, MAR, 2008, RCR, "3dmerge", MINOR, TYPE_GENERAL, 10138 "added some examples to the -help output", 10139 NULL 10140 } , 10141 10142 { 11, MAR, 2008, RCR, "model_demri_3", MINOR, TYPE_NEW_OPT, 10143 "added control of hematocrit via AFNI_MODEL_D3_HCT", 10144 NULL 10145 } , 10146 10147 { 10, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_NEW_ENV, 10148 "AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library", 10149 "The default is 1, 0 is quiet, and values go up to 7." 10150 } , 10151 10152 { 10, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_GENERAL, 10153 "AFNI can read/write .gii.dset as with .gii", 10154 NULL 10155 } , 10156 10157 { 10, MAR, 2008, RCR, "Dimon", MINOR, TYPE_NEW_OPT, 10158 "applied -gert_outdir in the case of dicom images", 10159 NULL 10160 } , 10161 10162 { 10, MAR, 2008, RCR, "Dimon", MINOR, TYPE_MODIFY, 10163 "if only 1 run, GERT_Reco_dicom is named per run", 10164 NULL 10165 } , 10166 10167 { 10, MAR, 2008, RCR, "SUMA_SurfMeasures", MAJOR, TYPE_BUG_FIX, 10168 "averages did not include nodes lost to -cmask", 10169 "Noticed by M Beauchamp." 10170 } , 10171 10172 { 7, MAR, 2008, RCR, "make_stim_times.py", MINOR, TYPE_BUG_FIX, 10173 "properly ignore empty lines, and exit on short files", 10174 NULL 10175 } , 10176 10177 { 6, MAR, 2008, RCR, "GIFTI", MICRO, TYPE_MODIFY, 10178 "allow functional control over GIFTI encoding" , 10179 NULL 10180 } , 10181 10182 { 5, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_BUG_FIX, 10183 "fixed passing of INDEX_LIST" , 10184 NULL 10185 } , 10186 10187 { 5, MAR, 2008, RCR, "GIFTI", MINOR, TYPE_MODIFY, 10188 "do not duplicate data when reading and writing GIFTI from AFNI", 10189 NULL 10190 } , 10191 10192 { 4, MAR, 2008, RCR, "3dTstat", MINOR, TYPE_NEW_OPT, 10193 "added -accumulate option, to output each partial sum" , 10194 "for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k" 10195 } , 10196 10197 { 3, MAR, 2008, RCR, "website", MINOR, TYPE_MODIFY, 10198 "updated the AFNI History website pages, with a table of entries", 10199 NULL 10200 } , 10201 10202 { 29, FEB, 2008, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 10203 "added a TYPE, -type, a new level, and a string to identify each level", 10204 NULL 10205 } , 10206 10207 { 28, FEB, 2008, RCR, "afni_history", MINOR, TYPE_NEW_OPT, 10208 "added -list_authors option and adjusted spacing", 10209 NULL 10210 } , 10211 10212 { 27, FEB, 2008, RCR, "afni_history", SUPER, TYPE_NEW_PROG, 10213 "program to display the history of AFNI updates" , 10214 "This will be used to create a web page of AFNI updates.\n" 10215 "Please see 'afni_history -help' for more details." 10216 } , 10217 10218 { 27, FEB, 2008, RCR, "afni_proc.py", MINOR, TYPE_BUG_FIX, 10219 "fixed -regress_use_stim_files typo (was -regress_use_stim_times)", 10220 NULL 10221 } , 10222 10223 { 26, FEB, 2008, RCR, "afni_history", MICRO, TYPE_GENERAL, 10224 "checked in initial afni_history files", 10225 NULL 10226 } , 10227 10228 { 25, FEB, 2008, RCR, "plug_vol2surf", MAJOR, TYPE_BUG_FIX, 10229 "fixed application of cluster for sending data to suma", 10230 10231 "Previously, clustering was only applied when the Olay and Thr sub-bricks\n" 10232 "were the same." 10233 } , 10234 10235 { 24, FEB, 2008, RCR, "GIFTI", MINOR, TYPE_MODIFY, 10236 "GIFTI library now considers MetaData without Value as valid", 10237 10238 NULL 10239 } , 10240 10241 /* pre-afni_history updates, mostly new programs and data formats */ 10242 10243 { 21, FEB, 2008, RCR, "GIFTI", SUPER, TYPE_GENERAL, 10244 "AFNI programs can now read and write GIFTI datasets", 10245 10246 "GIFTI datasets are for data in the surface domain, with file suffix .gii.\n" 10247 "Support must be requested at compile time, and it requires libexpat.\n" 10248 "Please see http://www.nitrc.org/projects/gifti for many details." 10249 } , 10250 10251 { 6, FEB, 2008, RCR, "3dbucket", MINOR, TYPE_GENERAL, 10252 "modified to copy FDR curves", 10253 NULL 10254 } , 10255 10256 { 22, JAN, 2008, RCR, "afni_proc.py", MINOR, TYPE_NEW_OPT, 10257 "added options to estimate smoothness in data for use in AlphaSim", 10258 "See help options -regress_est_blur_epits and -regress_est_blur_errts." 10259 } , 10260 10261 { 28, DEC, 2007, RCR, "gifti_tool", MAJOR, TYPE_NEW_PROG, 10262 "program to read and write GIFTI datasets", 10263 NULL 10264 } , 10265 10266 { 3, DEC, 2007, RCR, "GIFTI", MAJOR, TYPE_GENERAL, 10267 "initial release of gifti I/O C API", 10268 NULL 10269 } , 10270 10271 { 31, AUG, 2007, RCR, "DECONFLICT", MAJOR, TYPE_MODIFY, 10272 "modified default behavior of programs from deconflict to no overwrite", 10273 "See AFNI_DECONFLICT in README.environment." 10274 } , 10275 10276 { 31, AUG, 2007, RCR, "model_conv_diffgamma", MINOR, TYPE_NEW_PROG, 10277 "NLfim model to compute the convolution of the difference of gammas", 10278 NULL 10279 } , 10280 10281 { 30, JUL, 2007, RCR, "regression_tests", MAJOR, TYPE_GENERAL, 10282 "added setup for regression testing to NIFTI package", 10283 "This can be used as a template for testing any command-line programs." 10284 } , 10285 10286 { 20, DEC, 2006, RCR, "afni_proc.py", SUPER, TYPE_NEW_PROG, 10287 "program to write complete single subject FMRI processing script", 10288 NULL 10289 } , 10290 10291 { 11, DEC, 2006, RCR, "make_stim_times.py", MINOR, TYPE_NEW_PROG, 10292 "program to convert stim_files to stim_times files", 10293 NULL 10294 } , 10295 10296 { 22, OCT, 2006, RCR, "model_demri_3", MAJOR, TYPE_NEW_PROG, 10297 "NLfim model for Dynamic Enhanced MRI", 10298 NULL 10299 } , 10300 10301 { 12, OCT, 2006, RCR, "serial_writer", MINOR, TYPE_NEW_PROG, 10302 "program to send data from a file, pipe or made up to a given serial port", 10303 NULL 10304 } , 10305 10306 { 8, AUG, 2006, RCR, "C++", MINOR, TYPE_MODIFY, 10307 "afni program compiles in C++ (effort with Rich and Greg Balls)", 10308 NULL 10309 } , 10310 10311 { 3, AUG, 2006, RCR, "NI_SURF_DSET", SUPER, TYPE_GENERAL, 10312 "added a new surface dataset format, with read/write ability in AFNI", 10313 NULL 10314 } , 10315 10316 { 25, JAN, 2006, RCR, "model_michaelis_menton", MAJOR, TYPE_NEW_PROG, 10317 "NLfim model function for ethanol studies", 10318 NULL 10319 } , 10320 10321 { 2, DEC, 2005, RCR, "ANOVA", SUPERDUPER, TYPE_MODIFY, 10322 "changed variance computations in 3dANOVA programs to not assume sphericity", 10323 "For details, see https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html ." 10324 } , 10325 10326 { 11, OCT, 2005, RCR, "3dmaxima", MAJOR, TYPE_NEW_PROG, 10327 "command-line version of maxima plugin", 10328 NULL 10329 } , 10330 10331 { 5, JUL, 2005, RCR, "Dimon", SUPER, TYPE_NEW_PROG, 10332 "program to monitor real-time acquisition of DICOM images", 10333 NULL 10334 } , 10335 10336 { 25, APR, 2005, RCR, "NIFTI", SUPER, TYPE_GENERAL, 10337 "AFNI can read and write NIFTI datasets (effort with Bob and Rich)", 10338 NULL 10339 } , 10340 10341 { 7, JAN, 2005, RCR, "nifti_tool", SUPER, TYPE_NEW_PROG, 10342 "program to directly manipulate or compare NIFTI dataset headers", 10343 NULL 10344 } , 10345 10346 { 7, JAN, 2005, RCR, "NIFTI", SUPER, TYPE_GENERAL, 10347 "initial release of NIFTI library", 10348 NULL 10349 } , 10350 10351 { 4, OCT, 2004, RCR, "vol2surf", SUPER, TYPE_GENERAL, 10352 "added vol2surf interface for real-time mapping from afni to suma", 10353 NULL 10354 } , 10355 10356 { 31, MAR, 2004, RCR, "serial_helper", MAJOR, TYPE_NEW_PROG, 10357 "program to pass realtime registration params from TCP to serial port", 10358 NULL 10359 } , 10360 10361 { 1, DEC, 2003, RCR, "SurfMeasures", MAJOR, TYPE_NEW_PROG, 10362 "program to compute various measures over surfaces", 10363 NULL 10364 } , 10365 10366 { 5, AUG, 2003, RCR, "3dVol2Surf", SUPER, TYPE_NEW_PROG, 10367 "program to map data from the volume to domain to the surface domain", 10368 NULL 10369 } , 10370 10371 { 29, MAY, 2003, RCR, "3dSurf2Vol", SUPER, TYPE_NEW_PROG, 10372 "program to map data from the surface domain to the volume domain", 10373 NULL 10374 } , 10375 10376 { 15, JAN, 2003, RCR, "Imon", MAJOR, TYPE_NEW_OPT, 10377 "added connection to the realtime plugin in afni", 10378 NULL 10379 } , 10380 10381 { 27, NOV, 2002, RCR, "Imon", SUPER, TYPE_NEW_PROG, 10382 "program to monitor GE I-files as they are written to the scanner", 10383 NULL 10384 } , 10385 10386 { 1, OCT, 2002, RCR, "file_tool", SUPER, TYPE_NEW_PROG, 10387 "program to perform generic manipulations of binary files", 10388 NULL 10389 } , 10390 10391 { 20, JUN, 2002, RCR, "@make_stim_file", MINOR, TYPE_NEW_PROG, 10392 "script to create binary stim files", 10393 NULL 10394 } , 10395 10396 { 6, JUN, 2002, RCR, "@SUMA_Make_Spec_FS", MAJOR, TYPE_NEW_PROG, 10397 "script to import FreeSurfer surfaces into SUMA", 10398 NULL 10399 } , 10400 10401 { 21, MAY, 2002, RCR, "3dresample", SUPER, TYPE_NEW_PROG, 10402 "program to change a dataset orientation and/or grid spacing", 10403 NULL 10404 } , 10405 10406 { 8, MAR, 2002, RCR, "plug_crender", SUPER, TYPE_NEW_PROG, 10407 "added rendering plugin to afni", 10408 NULL 10409 } , 10410 10411 { 99,99,99, NULL,NULL, 99,99, NULL,NULL} /** the end (do not delete) **/ 10412 } ; 10413