Kayle's Reference Guide
To delete group maps within each subject's functional directory (from your functional dir):
find . -name females_FE -print0| xargs -0 rm -rdv >& rm_females_FE.log
To set up tunneling for VNC: http://www.martinos.org/martinos/userInfo/computer/remoteAccess.php
vnccheck /usr/pubsw/bin/vncserver.glx ssh -L5901:baobab:5901 username@entry.nmr.mgh.harvard.edu ssh -L5901:ficus:5902 username@entry.nmr.mgh.harvard.edu For your VNC program, connect to localhost:1 or localhost:5901, and enter your vnc password, set with the command vncpasswd.
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 and consistent with logbook 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 &
My scripts: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/kslays