You can use a virtual frame buffer. I wrote a frontend for one to do
just this
here is the help
# fsxvfb - a simple application of the virtual frame buffer (vrb) for
# X This can run graphical commands in a "headless" way, ie, without
# needing to create a window. This can be handy when you want to, eg,
# create images using freeview but you don't want windows continuously
# popping up. Just run something like:
# "fsxvrb freeview -v orig.mgz -viewport x -ss pic1.jpg"
# This script has a procedure for looking for an open display port
# starting at 10. The port is relinquished after the command
# finishes. Ports are locked if the file /tmp/.X$D-lock (where $D is
# the display) exists or a previous Xvfb launched with the port is
# still running. If this file exists, then that display cannot be
# used. This can happen if the command does not return and you kill it
# (it should handle control-c ok). You can always delete the lock
# file and kill the Xvfb by hand. Rebooting will also clean things
# up.
On 12/2/2024 3:32 PM, Blujus, Jenna wrote:
External Email - Use Caution
Hello,
I have run vertex-wise cortical thickness analyses via command line
(mris_preproc, mri_glmfit, mri_glmfit-sim) using Freesurfer v7.3.2
(freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275). I am now
attempting to take a screenshot of the resulting significant clusters
with Freeview.
I am running multiple analyses so I set up an sbatch job to be
submitted via our hpc cluster scheduler. The issue is that GUIs can't
be launched via sbatch, so no screenshot is generated. I could do this
via command line but I was hoping to automate the process. Is there
any flag added or alternative approach that can be taken to generate
the screenshot via sbatch jobs?
Below is the command:
freeview -f
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:overlay=lh.gender.glmdir/group.diff/cache.th30.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.gender.glmdir/group.diff/cache.th30.abs.sig.ocn.annot
-viewport 3d -layout 1 -hide-3d-slices -hide-3d-frames -cam azimuth
180 -ss
${script_dir}/results_summary/results-${parent_folder}_${iv}_${crnt_combo}_med.jpg
Error when run via sbatch:
could not connect to display :1.0
This application failed to start because no Qt platform plugin could
be initialized. Reinstalling the application may fix this problem.
Thanks,
Jenna
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