:orphan: .. _ahelp_@snapshot_volreg: **************** @snapshot_volreg **************** .. contents:: :local: | .. code-block:: none ----------------------------------------------------------------- This script will make a JPEG image showing the edges of an EPI dataset overlay-ed on an anatomical dataset. The purpose is to let the user (you) judge the quality of the 3D registration. Three images from each of the coronal, axial, and sagittal AFNI image viewers are used, laid out in a 3x3 grid. @snapshot_volreg works by running the AFNI GUI inside a "virtual" X11 display server program named "Xvfb", and saving images from that copy of AFNI. The script also uses programs from the netpbm11 software library to put the saved images together into a pleasing layout. If the script cannot find the netpbm11 software, it will not run :( ----------------------------------------------------------------- Usage: @snapshot_volreg ANATdataset EPIdataset [jname] [xdisplay] Sample (from an afni_proc.py results directory): @snapshot_volreg anat_final.sub-10506+tlrc \ pb02.sub-10506.r01.volreg+tlrc sub-10506 The output file from this example is "sub-10506.jpg". ----------------------------------------------------------------- Do NOT put a sub-brick index (such as "[0]") on the EPIdataset name -- the script will automatically only use the "[0]" volume. (( Although the original use was for visualizing how well EPI )) (( and anatomical datasets were aligned by align_epi_anat.py, )) (( it is also useful to see how well 3dQwarp aligned an )) (( anatomical dataset to a template dataset. )) The optional third argument is the name of the output JPEG file -- if it does not end in ".jpg", that suffix will be added. If you do NOT supply a 3rd argument, the script will invent a name: it is probably better for you to supply a 3rd argument. It is now permitted to include an output path as part of the third argument. The fourth (and very optional) argument is the display number of an ALREADY RUNNING copy of Xvfb, as in Xvfb :88 -screen 0 1024x768x24 & If you do NOT supply this number (88 in the example), then the script will start its own Xvfb (on a display of its choosing), use it once, and then stop it. If you are going to run this script many times in a row, starting and stopping your own Xvfb instance will speed things up a little. Normally, you do not need to use this 4th argument. ----------------------------------------------------------------- The edges from a typical EPI dataset are usually broken up and do not completely outline sulci, ventricles, etc. In judging the quality of alignment, I usually start by looking at the outlines of the large lateral ventricles -- if those are very wrong, the alignment is not good. After that, I look at the sulci in the superior part of the brain -- if the EPI edges there seem to be mostly aligned with the sulci, then I am usually happy. The base of the brain, where lots of EPI dropout happens, often does not not show good edge alignment even when the rest of the brain alignment looks good. ----------------------------------------------------------------- If this script crashes, then it might leave behind files with names that start with "zzerm". Delete these files. It is also possible that the Xvfb program will still be running if this script crashes. A command such as that below can be used to see if you have any stray Xvfb programs running: ps X | grep Xvfb | grep -v grep If there are any such programs, the command below can be used to kill all of them: killall Xvfb -------------- Author: The Madd Allineator ----------------------