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startup.sh
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startup.sh
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#! /bin/bash
echo "Setting the environment ..."
source $FREESURFER_HOME/SetUpFreeSurfer.sh
#export SUBJECTS_DIR=/output
echo "Run x server to run GUI"
# while [ "$subj_path" != 0 ]
# do
# subj_path=0
# cd /input && subj_path="$(zenity --file-selection --title="Choose a directory" --directory)"
# freeview -v $subj_path/mri/T1.mgz -f \
# $subj_path/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=1,6.5:overlay_color='colorwheel','inverse'::name=lh_thickness \
# $subj_path/surf/rh.inflated:overlay=rh.thickness:overlay_threshold=1,6.5:overlay_color='colorwheel','inverse'::name=rh_thickness \
# $subj_path/surf/rh.white:edgethickness=1:hide_in_3d='true' \
# $subj_path/surf/rh.pial:edgethickness=1:hide_in_3d='true' \
# $subj_path/surf/lh.white:edgethickness=1:hide_in_3d='true' \
# $subj_path/surf/lh.pial:edgethickness=1:hide_in_3d='true' \
# --hide-3d-slices --viewport 3d -layout 4
# done
#freeview -f good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
#good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
#good_output/surf/lh.inflated:visible=0 \
#good_output/surf/lh.white:visible=0 \
#good_output/surf/lh.pial \
#--viewport 3d