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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 :(
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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".
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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.
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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.
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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 ----------------------
