1#!/bin/tcsh 2 3@global_parse `basename $0` "$*" ; if ($status) exit 0 4 5# [PT: July 2, 2018] 6# + Edited to allow for inclusion of path when naming output JPGs 7# 8# [PT: Mar 6, 2020] 9# + note about updating PBAR_ALL, which doesn't appear necessary at the 10# moment, just based on how outputs look currently 11# + added '-no1D' to the afni command, to remove annoying warnings if there 12# happens to be a *.1D file lurking 13# + add in disable IMSAVE warnings with env var 14# + make the GUI run quietly (-q) 15# + set many other env vars to be quieter. 16 17# help? 18 19if ( $#argv < 2 ) then 20 echo 21 echo '-----------------------------------------------------------------' 22 echo 23 echo 'This script will make a JPEG image showing the edges of an' 24 echo 'EPI dataset overlay-ed on an anatomical dataset. The purpose is' 25 echo 'to let the user (you) judge the quality of the 3D registration.' 26 echo 27 echo 'Three images from each of the coronal, axial, and sagittal' 28 echo 'AFNI image viewers are used, laid out in a 3x3 grid.' 29 echo 30 echo '@snapshot_volreg works by running the AFNI GUI inside a "virtual"' 31 echo 'X11 display server program named "Xvfb", and saving images from' 32 echo 'that copy of AFNI. The script also uses programs from the netpbm11' 33 echo 'software library to put the saved images together into a pleasing' 34 echo 'layout. If the script cannot find the netpbm11 software, it will' 35 echo 'not run :(' 36 echo 37 echo '-----------------------------------------------------------------' 38 echo 'Usage: @snapshot_volreg ANATdataset EPIdataset [jname] [xdisplay]' 39 echo 40 echo 'Sample (from an afni_proc.py results directory):' 41 echo 42 echo ' @snapshot_volreg anat_final.sub-10506+tlrc \' 43 echo ' pb02.sub-10506.r01.volreg+tlrc sub-10506' 44 echo 45 echo 'The output file from this example is "sub-10506.jpg".' 46 echo '-----------------------------------------------------------------' 47 echo 48 echo 'Do NOT put a sub-brick index (such as "[0]") on the EPIdataset' 49 echo 'name -- the script will automatically only use the "[0]" volume.' 50 echo 51 echo '(( Although the original use was for visualizing how well EPI ))' 52 echo '(( and anatomical datasets were aligned by align_epi_anat.py, ))' 53 echo '(( it is also useful to see how well 3dQwarp aligned an ))' 54 echo '(( anatomical dataset to a template dataset. ))' 55 echo 56 echo 'The optional third argument is the name of the output JPEG' 57 echo 'file -- if it does not end in ".jpg", that suffix will be added.' 58 echo 'If you do NOT supply a 3rd argument, the script will invent a name:' 59 echo 'it is probably better for you to supply a 3rd argument.' 60 echo 'It is now permitted to include an output path as part of the third' 61 echo 'argument.' 62 echo 63 echo 'The fourth (and very optional) argument is the display number' 64 echo 'of an ALREADY RUNNING copy of Xvfb, as in' 65 echo ' Xvfb :88 -screen 0 1024x768x24 &' 66 echo 'If you do NOT supply this number (88 in the example), then' 67 echo 'the script will start its own Xvfb (on a display of its choosing),' 68 echo 'use it once, and then stop it. If you are going to run this script' 69 echo 'many times in a row, starting and stopping your own Xvfb' 70 echo 'instance will speed things up a little. Normally, you do not' 71 echo 'need to use this 4th argument.' 72 echo 73 echo '-----------------------------------------------------------------' 74 echo 75 echo 'The edges from a typical EPI dataset are usually broken up and' 76 echo 'do not completely outline sulci, ventricles, etc. In judging' 77 echo 'the quality of alignment, I usually start by looking at the' 78 echo 'outlines of the large lateral ventricles -- if those are very' 79 echo 'wrong, the alignment is not good. After that, I look at the' 80 echo 'sulci in the superior part of the brain -- if the EPI edges' 81 echo 'there seem to be mostly aligned with the sulci, then I am' 82 echo 'usually happy. The base of the brain, where lots of EPI' 83 echo 'dropout happens, often does not not show good edge alignment' 84 echo 'even when the rest of the brain alignment looks good.' 85 echo 86 echo '-----------------------------------------------------------------' 87 echo 88 echo 'If this script crashes, then it might leave behind files with' 89 echo 'names that start with "zzerm". Delete these files.' 90 echo 'It is also possible that the Xvfb program will still be running' 91 echo 'if this script crashes. A command such as that below can' 92 echo 'be used to see if you have any stray Xvfb programs running:' 93 echo 94 echo ' ps X | grep Xvfb | grep -v grep' 95 echo 96 echo 'If there are any such programs, the command below can be used' 97 echo 'to kill all of them:' 98 echo 99 echo ' killall Xvfb' 100 echo 101 echo '-------------- Author: The Madd Allineator ----------------------' 102 echo 103 exit 0 104endif 105 106# control variables 107 108setenv AFNI_DONT_LOGFILE YES 109unset noclobber 110 111# check if all the needed auxiliary programs exist 112 113set nerr = 0 114set errm = "** ERROR:" 115 116set plist = ( Xvfb djpeg cjpeg pnmcat pbmtext pnmscale pbmtopgm ) 117foreach pppp ( $plist ) 118 set wwww = `which $pppp` 119 if ( $status != 0 ) then 120 @ nerr++ 121 set errm = "$errm $pppp" 122 endif 123end 124 125# we can use either pamcomp or pnmcomp, so only need to 126# find one of the twain 127 128set pcprog = pamcomp 129set wwww = `which $pcprog` 130if ( $status != 0 ) then 131 set pcprog = pnmcomp 132 set wwww = `which $pcprog` 133 if ( $status != 0 ) then 134 @ nerr++ 135 set errm = "$errm (pnmcomp OR pamcomp)" 136 endif 137endif 138 139if ( $nerr > 0 ) then 140 echo "$errm -- not found in path -- @snapshot_volreg fails" 141 echo "** WARNING: this script cannot run without installing package netpbm11" 142 exit 1 143endif 144 145# set the prefix for the anat and epi datasets 146 147set adset = $argv[1] 148set abase = $adset:t 149set anat = `basename $abase .gz` 150set anat = `basename $anat .nii` 151set anat = `basename $anat .HEAD` 152set anat = `basename $anat .BRIK` 153set anat = `basename $anat +tlrc` 154set anat = `basename $anat +orig` 155set anat = `basename $anat +acpc` 156set anat = `basename $anat +tlrc.` 157set anat = `basename $anat +orig.` 158set anat = `basename $anat +acpc.` 159if ( $abase == $anat.nii.gz ) then 160 set asuff = .nii.gz 161else if ( $abase == $anat.nii ) then 162 set asuff = .nii 163else 164 set asuff = "" 165endif 166 167set edset = $argv[2] 168set epi = `basename $edset .gz` 169set epi = `basename $epi .nii` 170set epi = `basename $epi .HEAD` 171set epi = `basename $epi .BRIK` 172set epi = `basename $epi +orig` 173set epi = `basename $epi +acpc` 174set epi = `basename $epi +tlrc` 175set epi = `basename $epi +tlrc.` 176set anat = `basename $anat +tlrc.` 177set anat = `basename $anat +tlrc` 178set anat = `basename $anat +orig.` 179set anat = `basename $anat +acpc.` 180 181# set output image prefix 182 183if ( $#argv > 2 ) then 184 # [PT: July 2, 2018] Include output path with filename 185 set jdir = `dirname $argv[3]` 186 187 set jnam = $argv[3] 188 set jnam = `basename "$jnam" .jpg` 189 set jnam = `basename "$jnam" .JPG` 190 set jnam = `basename "$jnam" .jpeg` 191 set jnam = `basename "$jnam" .JPEG` 192else 193 set jdir = "." 194 set jnam = $anat.$epi 195endif 196 197# Are we re-using Xvfb? 198 199unset xdisplay 200unset killX 201if ( $#argv > 3 ) then 202 set xdisplay = $argv[4] 203 if ( ! -e /tmp/.X${xdisplay}-lock ) then 204 echo "** ERROR: it doesn't look like Xvfb is running with display $xdisplay" 205 exit 1 206 endif 207endif 208 209set exad = `3dinfo -exists $adset` 210set exep = `3dinfo -exists $edset` 211 212if ( $exad == 0 || $exep == 0 ) then 213 if ( $exad == 0 ) echo "** ERROR: @snapshot_volreg can't find $adset" 214 if ( $exep == 0 ) echo "** ERROR: @snapshot_volreg can't find $edset" 215 exit 1 216endif 217 218# set some AFNI GUI things 219 220setenv AFNI_NOSPLASH YES 221setenv AFNI_SPLASH_MELT NO 222setenv AFNI_LEFT_IS_LEFT YES 223setenv AFNI_IMAGE_LABEL_MODE 5 224setenv AFNI_IMAGE_LABEL_SIZE 2 225setenv AFNI_ENVIRON_WARNINGS NO 226setenv AFNI_COMPRESSOR NONE 227setenv AFNI_IMSAVE_WARNINGS NO 228setenv AFNI_NEVER_SAY_GOODBYE YES 229setenv AFNI_STARTUP_WARNINGS NO 230setenv AFNI_MOTD_CHECK NO 231 232# start the X virtual frame buffer on display #xdisplay 233 234set ranval = `count -dig 1 1 999999 R1` 235 236if ( $?xdisplay == 0 ) then 237 set killX = 1 238 set ntry = 1 239 set Xnotfound = 1 240 while( $Xnotfound ) 241 set xdisplay = `count -dig 1 3 999 R1` 242 if ( -e /tmp/.X${xdisplay}-lock ) continue 243 echo " -- trying to start Xvfb :${xdisplay}" 244 Xvfb :${xdisplay} -screen 0 1024x768x24 >& /dev/null & 245 sleep 2 246 jobs > zzerm.$ranval.txt 247 grep -q Xvfb zzerm.$ranval.txt 248 set Xnotfound = $status 249 \rm -f zzerm.$ranval.txt 250 if ( $Xnotfound == 0 )break ; 251 killall Xvfb ; sleep 1 252 @ ntry++ 253 if ( $ntry > 9 ) then 254 echo "** ERROR: can't start Xvfb -- exiting" 255 exit 1 256 endif 257 end 258endif 259 260setenv DISPLAY :${xdisplay} 261 262# quasi-random temp filename prefix 263 264set zpref = zzerm.X${xdisplay}-${ranval} 265 266# crop the input anat to a standard size 267 268set cdset = ${zpref}.acrop.nii 269 2703dAutobox -npad 17 -prefix $cdset $adset 271 272# resample the EPI to the anat grid 273 2743dAllineate -input ${edset}'[0]' \ 275 -master ${cdset} \ 276 -prefix ${zpref}.epiR.nii \ 277 -1Dparam_apply IDENTITY \ 278 -final cubic 279 280set Rnam = ${zpref}.epiR.nii 281 282# aniso- or median-smooth the resampled EPI 283 284if ( 0 ) then 285 3danisosmooth -iters 2 -prefix ${zpref}.epiRS.nii ${zpref}.epiR.nii 286 set Rnam = ${zpref}.epiRS.nii 287else 288 3dMedianFilter -irad 1.01 -iter 1 -prefix ${zpref}.epiRS.nii ${zpref}.epiR.nii 289 set Rnam = ${zpref}.epiRS.nii 290endif 291 292# find edges in the EPI 293 2943dedge3 -input $Rnam -prefix ${zpref}.epiE.nii 295 296# get the EPI automask and apply it to the edgized EPI 297 2983dAutomask -q -prefix ${zpref}.epiM.nii -clfrac 0.333 -dilate 5 $Rnam 2993dcalc -a ${zpref}.epiE.nii -b ${zpref}.epiM.nii -expr 'a*b' -prefix ${zpref}.epiEM.nii 300 301# get the lower and upper thresholds for the edgized EPI 302 303set epp = `3dBrickStat -non-zero -percentile 20 60 80 ${zpref}.epiEM.nii` 304set eth = $epp[2] 305set emx = $epp[4] 306 307# run AFNI to make the 3 overlay images 308 309set anatCM = ( `3dCM $cdset` ) 310 311set anatNN = `3dinfo -nijk $cdset` 312 313set astep = `ccalc -int "cbrt($anatNN)/6.111"` 314 315if ( $astep < 2 ) then 316 set astep = 2 317endif 318 319# [PT] NB: at some point, it may become necessary to adjust this line: 320## -com "SET_PBAR_ALL +99 1 Plasma" \ 321# ... but at present, things tend to look good as they are. For that 322# future generation, you could perhaps use 3dBrickStat to get an 323# appropriate top_val for the PBAR_ALL 324 325echo "++ Start GUI to snapshot" 326 327afni -q -noplugins -no_detach -no1D \ 328 -DAFNI_DEFAULT_OPACITY=9 \ 329 -DAFNI_FUNC_ALPHA=Linear \ 330 -com "SWITCH_UNDERLAY ${cdset}" \ 331 -com "SWITCH_OVERLAY ${zpref}.epiEM.nii" \ 332 -com "SET_DICOM_XYZ $anatCM" \ 333 -com "SET_PBAR_ALL +99 1 Plasma" \ 334 -com "SET_FUNC_RANGE $emx" \ 335 -com "SET_THRESHNEW $eth *" \ 336 -com "SEE_OVERLAY +" \ 337 -com "SET_XHAIRS OFF" \ 338 -com "OPEN_WINDOW sagittalimage opacity=6 mont=3x1:$astep" \ 339 -com "OPEN_WINDOW axialimage opacity=6 mont=3x1:$astep" \ 340 -com "OPEN_WINDOW coronalimage opacity=6 mont=3x1:$astep" \ 341 -com "SAVE_JPEG sagittalimage ${zpref}.sag.jpg blowup=2" \ 342 -com "SAVE_JPEG coronalimage ${zpref}.cor.jpg blowup=2" \ 343 -com "SAVE_JPEG axialimage ${zpref}.axi.jpg blowup=2" \ 344 -com "QUITT" \ 345 ${cdset} ${zpref}.epiEM.nii 346 347# convert the output JPEGs to PNMs for manipulation 348 349djpeg ${zpref}.sag.jpg > ${zpref}.sag.pnm 350djpeg ${zpref}.cor.jpg > ${zpref}.cor.pnm 351djpeg ${zpref}.axi.jpg > ${zpref}.axi.pnm 352 353# cat them together, make a text label, overlay it, make output JPEG 354 355pnmcat -tb -jcenter -black ${zpref}.sag.pnm ${zpref}.axi.pnm ${zpref}.cor.pnm > ${zpref}.pnm 356pbmtext -builtin fixed "$jnam" | pnmcrop | pbmtopgm 1 1 | pnmscale 2 > ${zpref}.t1.pgm 357pbmtext -builtin fixed "<- Left" | pbmtopgm 1 1 > ${zpref}.t2.pgm 358$pcprog -align=right -valign=bottom ${zpref}.t1.pgm ${zpref}.pnm > ${zpref}.t3.pnm 359$pcprog -align=right -valign=top ${zpref}.t2.pgm ${zpref}.t3.pnm | cjpeg -quality 95 > "$jdir/$jnam.jpg" 360 361# delete the trash data 362 363\rm -f ${zpref}.* 364 365echo "@snapshot_volreg output image = $jdir/$jnam.jpg" 366 367# stop Xvfb if we started it ourselves 368 369if ( $?killX ) kill %1 370 371exit 0 372
