115 November 2004: 2 * Created 3dTeig.c. Program calculates eigenvalues,vectors,FA from DTI data and 3 creates output brik file. Used 3dTstat.c as model for program. 4 * Rename 3dTeig.c 3dDTeig.c. Made program more efficient. Reduced width of help 5 to fit in 80 characters. 617 November 2004 7 * Renamed some internal messages and history to have the updated function name. 82 December 2004 9 * Created 3dDWItoDT.c. Program calculates diffusion tensor data from diffusion weighted images. 10 1120 December 2004 12 * Fixed bugs for initializing and freeing vectors in 3dDTeig timeseries 13 function that would sometimes result in segment faults 14 1523 December 2004 16 * Automask option now working in 3dDWItoDT. 17 1806 March 2005 19 * 3dDTeig.c modified to allow input datasets of at least 6 sub-briks (not necessarily equal to 6). 20 2128 March 2005 22 * 3dDWItoDT.c modified to include non-linear gradient descent method and several new options including eigenvalue,eigenvector calculations, debug briks, cumulative wts, reweighting, verbose output 23 2411 April 2005 25 * Moved ENTRY statements in 3dDWItoDT.c to come after variable declarations in 3 functions 26 2712 April 2005 28 * Added AFNI NIML graphing of convergence to 3dDWItoDT.c with user option -drive_afni nnnnn 29 3014 April 2005 31 * Fixed bug in 3dDWItoDT.c when user requests both linear solution and eigenvalues. Removed several unused ifdef'ed debugging code sections. 32 3320 April 2005 34 * slight modifications to comments in 3dDWItoDT.c for doxygen and consistent warnings and error messages 35 * Milwaukee in afni_func.c 36 3728 April 2005 38 * trivial program, 3dMax, for finding the minimum and maximum for a dataset 39 402 May 2005 41 * updated formerly trivial program (now only semi-trivial), 3dMax, to calculate means, use a mask file, do automasking. The program now includes scale factors for sub-briks and extends the types of allowable datasets 42 433 May 2005 44 * fixed checking of options for incompatibilities and defaults in 3dMax 45 464 May 2005 47 * added Mean diffusivity computation to 3dDWItoDT.c and 3dDTeig.c. Also in 3dDWItoDT.c, added an additional I0 (Ideal image voxel value) sub-brik included with debug_briks option. The I0 will be used as a basis for a test model dataset. Also fixed bug in masked off area for eigenvalues when using debug_briks. 48 4912 May 2005 50 * added count, negative, positive, zero options to 3dMax and fixed bug there in the calculation of a mean with a mask 51 * created 3dDTtoDWI.c to calculate ideal diffusion weighted images from diffusion tensors for testing purposes 52 5316 May 2005 54 * added tiny, tiny change to allow non_zero option with 3dMax 55 5619 May 2005 57 * added min and max limits to 3dhistog.c 58 5927 May 2005 60 * added mask option to 3dDWItoDT and fixed bug with automask for float dsets 61 * added initialization to pointer in 3dMax 62 6315 June 2005 64 * removed exits in plug_3Ddump_V2.c, plug_stavg.c, plug_edit.c, plug_volreg.c, plug_L1fit.c, plug_lsqfit.c, plug_power.c to prevent plug-ins from crashing AFNI application 65 * created new program, 3dAFNItoRaw, to create raw dataset of multiple sub-brik alternating at each voxel rather than at each volume 6616 June 2005 67 * fixed small typo in help for 3dMax.c 6824 June 2005 69 * created new program, DTIStudioFibertoSegments.c, to convert DTIStudio fiber files into SUMA segment files 7020 July 2005 71 * fixed bug for quick option for 3dMax 721 Aug 2005 73 * fixed bug in im2niml function in thd_nimlatr.c in testing for name field of images 747 Oct 2005 75 * Created anisosmooth program to do anisotropical smoothing of datasets (particularly DWI data). Current version is 2D only. 7618 Oct 2005 77 * Added 3D option to 3danisosmooth program. Fixed some bugs with near zero gradient and NaN eigenvector values and aiv viewer split window error. 78 * Fixed small bug in 3dMaskdump not allowing selection of last voxel in any dimension 7919 Oct 2005 80 * added support to 3dMax for checking for NaN,Inf and -Inf with the -nan and -nonan options 8120 Oct 2005 82 * fixed 3danisosmooth phi calculation for exponential version to use scaled eigenvalues 8318 Nov 2005 84 * made major changes to 3danisosmooth and DWIstructtensor to improve performance. 85 Also included changes for standardized message printing system for AFNI programs in 3danisosmooth.c, 86 DWIstructtensor.c, 3dMax.c, 3dDTeig.c, 3dDWItoDT.c 8721 Nov 2005 88 * fixed bug to improve efficiency of 3danisosmooth with mask datasets 8922 Nov 2005 90 * support for user options for level of Gaussian smoothing (-sigma1, -sigma2) in 3danisosmooth 9129 Nov 2005 92 * removed default author and version info for 3dMax. Now option -ver gives that 93 output. 3dMax is used in scripts, so that change confuses everything. 9414 Dec 2005 95 * added new options to 3danisosmooth for avoiding negative numbers and 96 fractional control of amount of edginess. 2D exponential method gives faster 97 results because of new constant and switched phi values. 9816 Dec 2005 99 * added new datum option to 3danisosmooth 10020 Dec 2005 101 * updated edt_blur.c to improve performance of y blurring on large images (nx>=512) 10221 Dec 2005 103 * minor update to edt_blur.c for slightly more compact code. 10413 Jan 2006 105 * added option to 3danisosmooth (-matchorig) to match range of original 106 voxels in each sub-brick. 10721 Feb 2006 108 * corrected some help for 1dcat program and generic help message used by other 109 1D programs. Updated help a bit for 3dmerge.c also. 11022 Feb 2006 111 * additional help updates for 1deval 1123 Apr 2006 113 * various fixes for Draw Dataset plug-in (datum check and label errors) 11420 Apr 2006 115 * update for 3dcopy to support writing NIFTI datasets 116 (Rick is responsible for this) 1174 May 2006 118 * fix for 3dROIstats.c for nzmedian and nzmean confusion 119 * erosion without redilation in thd_automask.c called in various places and 120 needs an additional parameter to continue redilating. 1219 May 2006 122 * 3dAutomask.c and thd_automask.c - stupid typos, debugging printfs removed, ... 12310 May 2006 124 * JPEG compression factor environment variable in several places 12519 Jun 2006 126 * byte swapping support for cross-platform conversion of DTI Studio fibers in 127DTIStudioFibertoSegments.Also updated warning and error messages to AFNI 128standards. Made help clearer for @DTI_studio_reposition. 12921 Jun 2006 130 * 3dNotes support for NIFTI file format and display of history notes 13122 Jun 2006 132 * 3dZcat updated to support NIFTI. edt_dsetitems had to be modified also for 133 duplication of .nii or .nii.gz suffix in file names. 134 * 3dDWItoDT can now make separate files for each type of output data to make it 135 easier to work with other packages. Lower diagonal order used for Dtensor to 136 make compliant with NIFTI standard in 3dDWItoDT and 3dDTeig. 137 29 Jun 2006 138 * fixed bug in edt_dsetitems.c that puts doubled .nii.nii or .nii.gz.nii.gz 139 extensions on filenames in some cases 140 * minor help changes in Draw Dataset plug-in (courtesy of Jill) 141 23 Aug 2006 142 * Updates to support NIFTI and gzipped NIFTI files in 3dZcat, 3daxialize, 3dCM, 143 3dNotes.Other changes in edt_dsetitems.c to support NIFTI format better. 144 * 3dDWItoDT supports Powell algorithm. 3dDTeig can read either old D tensor 145 order or new NIFTI standard D tensor order. It can also write out separate 146 files for eigenvalues, vectors, FA, MD (like 3dDWItoDT). 14724 Oct 2006 148 * Update to 3dNLfim to use memory mapping instead of shared memory, to support 149 multiple CPU jobs better 15025 Oct 2006 151 * 3dNLfim limit reports to every nth voxel via progress option 15226 Oct 2006 153 * model_zero, noise model,for removing noise modeling in 3dNLfim 15407 Nov 2006 155 * R1I mapping and voxel indexing support added to the DEMRI model,model_demri_3 15609 Nov 2006 157 * output datum type support in 3dNLfim 15808 Jan 2007 159 * 1dSEM program for doing structural equation modeling 16018 Jan 2007 161 * 1dSEM updates for growing model size over all possible models 16203 May 2007 163 * mri_read_dicom patches given and modified by Fred Tam for strange 164 Siemens DICOM headers 16504 May 2007 166 * minor output, option name and help changes to 1dSEM 16708 May 2007 168 * [with rickr] count can skip in a funny way 16909 May 2007 170 * minor changes to thd_mastery to allow simplified count commands in sub-brick 171selectors already implemented in thd_intlist.c and slightly modified help strings 172in 3ddata.h 17316 May 2007 174 * 1dSEM - changeable limits for connection coefficients 17529 May 2007 176 * oblique dataset handling. Bigger changes in mri_read_dicom, to3d, 3dWarp. 177Also smaller changes in thd_niftiwrite and read, 3ddata.h, vecmat.h, 178thd_dsetatrc, thd_dsetdblk.c 17904 Jun 2007 180 * Initialization bug in obliquity code on some systems, other minor changes 181for obliquity too 18206 Jun 2007 183 * NIFTI read creates oblique transformation structure 184 * minor fix to 1dSEM for tree growth stop conditions 18507 Jun 2007 186 * added ability for 3dWarp to obliquidate an already oblique dataset 18711 Jun 2007 188 * deeper searches for forest growth in 1dSEM with new leafpicker option. 189Compute cost of input coefficient matrix data in 1dSEM to verify published data with 190calccost option. Easier to read output data for 1dSEM (sqrmat.h) 19113 Jun 2007 192 * fixes for rewriting dataset header in 3dNotes, 3dCM and adwarp (effect of 193deconflicting changes) 19414 Jun 2007 195 * fixes for obliquity handling effects on non-oblique data in places, 196most obvious in NIFTI files where the coordinates are changed as in 3drefit, 1973dCM, 3drotate, 3dresample. Also fix for NIFTI reading of sform. 19818 Jun 2007 199 * duration, centroid and absolute sum calculations added to 3dTstat 20020 Jun 2007 201 * added -deoblique option to 3drefit to remove obliquity from dataset 20226 Jul 2007 203 * clarified help in 3dExtrema, and fixed a couple typos 20402 Aug 2007 205 * updated Talairach atlas for Eickhoff-Zilles 1.5 release 206 * updated help in whereami for clarification 20703 Aug 2007 208 * user input fix for 3dAutobox limits, added -noclust option too to keep any 209non-zero voxels 21006 Aug 2007 211 * 3dAutobox can also ignore automatic clip level 21227 Aug 2007 213 * modifications for 3dDWItoDT to improve handling of highly anisotropic voxels 214with new hybrid search method and bug fixes 21528 Aug 2007 216 * added b-value and allowed 0 values in MD and FA calculations 3dDTeig and 2173dDWItoDT 21807 Sep 2007 219 * updated viewer help to include newer keyboard and mouse shortcuts 22023 Sep 2007 221 * added some gray scales to overlay color scale choices, fixed small bug 222on lower limit of color scales in pbar.c and pbardefs.h. Also changed lowest 223index in cb_spiral, color-blind, color scale 22428 Sep 2007 225 * fixed a couple bugs in mri_read_dicom to add null termination to the string 226containing Siemens extra info and allowed for cross-product normals for vectors to 227to line up with slice positions when vectors are slightly off 1.0 22802 Oct 2007 229 * added memory and dataset write error checks to mri_read_dicom and to3d 23003 Oct 2007 231 * added non-zero mean option to 3dTstat 23209 Oct 2007 233 * added additional warning and error message handling to to3d 23414 Dec 2007 235 * added various monochrome lookup tables to overlay color scale choices 236including amber, red, green and blue (azure) 23723 Dec 2007 238 * put warnings in when using oblique datasets in AFNI GUI and when opening 239datasets elsewhere 240 * added another colorscale with amber/red/blue 24102 Jan 2008 242 * removed obliquity warnings when deobliquing with 3dWarp or 3drefit 24308 Jan 2008 244 * onset, offset (around maximum) added to 3dTstat 24509 Jan 2008 246 * volume added to 3dBrickStat 24710 Jan 2008 248 * fixed bug in 3dDTeig in eigenvalue calculation (no effect on results though) 24915 Jan 2008 250 * modified 1D file reading to allow for colons, alphabetic strings while 251maintaining support for complex (i) numbers 25205 Feb 2008 253 * added way to turn off pop-up warnings in afni GUI for obliquity and added 254another level of checking for obliquity transformation matrix in attributes 255 256 257