Reference Guide:
To delete group maps within each subject's functional directory:
find . -name females_FE -print0| xargs -0 rm -rdv >& rm_females_FE.log
To set up tunneling for VNC: vnccheck /usr/pubsw/bin/vncserver.glx ssh -L5901:baobab:5901 username@entry.nmr.mgh.harvard.edu
To run recon-all remotely:
#set up environment
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS_DIR TYPE_HERE
cd #PUT_YOUR_FUNCTIONAL_DIRECTORY_HERE
#find dicoms on bourget/archive
findsession %1
#output text summary
unpacksdcmdir -src PASTE_HERE -targ %1_sess -scanonly %1_scanonly
#copy config file from previous subject
cp TNC22_cfg %1_cfg
#view and confirm scan order is correct
emacs %1_cfg
#unpack data
nohup unpacksdcmdir -src PASTE_HERE -targ %1_sess -cfg %1_cfg -fsfast >& unpack%1.log &
#do remote overnight reconstruction
nohup recon-all -all -subjid %1 -i %1_sess/3danat/003 -i %1_sess/3danat/004 >& /dev/null &