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 &