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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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