'''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