Setup - Free Surfer Wiki

login as nmrclass
cleanup junk on desktop (just Computer, Home, Trash, Terminal and Firefox)
open Firefox:
- should open to FsTutorial
- change 'surfer' to 'carlo'
- test opening a tutorial wiki page, then a slide
open a terminal and su root
add this to the end of file /etc/rc.local:

netstatcode=`netstat -rn | grep 192.168.2.1`
if [ -n "$netstatcode" ] ; then
    mount 192.168.2.1:/Users/Shared /mnt/macmini
    sleep 4
fi
rm -f /home/nmrclass/practice/*

open a new terminal, then do this:

cd
rm .cshrc
pico .cshrc

then copy this text into editor:

# exit if not an interactive shell
if ($?USER == 0 || $?prompt == 0) exit

alias dir "ls -alF"

xset b off

setenv PATH "/sbin:/usr/sbin:/usr/local/bin":"$PATH"
if ( -e $HOME/bin) then
  setenv PATH "$HOME/bin":"$PATH"
endif

# in case not already mounted, supporting a connected USB HD
mount /media/disk >& /dev/null

# define path to mac mini server NFS mount of apps and data.
# this should be mounted at boot when /etc/rc.local was run.
set MYOS=(centos4_x86_64)
set NFSAPPS=(/mnt/macmini/apps)
set MYNAME=(`uname -n`)
set NFSDATA=(/mnt/macmini/RW_tutorial_data)

#
# FSL
#
if ( -e $NFSAPPS/$MYOS/fsl) then
  setenv FSLDIR $NFSAPPS/$MYOS/fsl
else
  if ( -e /home/apps/fsl) then
    setenv FSLDIR /home/apps/fsl
  endif
endif

#
# Freesurfer and FS-FAST
#
# data...
if ( -e $NFSDATA/$MYNAME/buckner_data ) then
  setenv TUTORIAL_DATA $NFSDATA/$MYNAME
else
  if ( -e /media/disk/buckner_data/tutorial_subjs ) then
    setenv TUTORIAL_DATA /media/disk/
  endif
endif
if ( $?TUTORIAL_DATA ) then
  setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
  setenv FSFTUTDIR $TUTORIAL_DATA/fsfast-tutorial.subjects
endif
# binaries...
if ( -e $NFSAPPS/$MYOS/freesurfer/SetUpFreeSurfer.csh ) then
  setenv FREESURFER_HOME $NFSAPPS/$MYOS/freesurfer
else
  if ( -e /home/apps/freesurfer/SetUpFreeSurfer.csh ) then
    setenv FREESURFER_HOME /home/apps/freesurfer
  endif
endif
# setup...
if ( $?FREESURFER_HOME ) then
  setenv FSF_OUTPUT_FORMAT nii.gz
  source $FREESURFER_HOME/SetUpFreeSurfer.csh
  echo "FSFTUTDIR         $FSFTUTDIR"
endif

#
# MATLAB
#
if ( -e $NFSAPPS/matlab/bin ) then
  setenv MATLABPATH $NFSAPPS/matlab
else
  if ( -e /home/apps/matlab/bin ) then
    setenv MATLABPATH /home/apps/matlab
  endif
endif
if ( $?MATLABPATH ) then
  setenv PATH "$MATLABPATH/bin":"$PATH"
endif

#
# Diffusion Toolkit and TrackVis
#
if ( -e $NFSAPPS/$MYOS/dtk ) then
  setenv DTK_HOME $NFSAPPS/$MYOS/dtk
else
  if ( -e /home/apps/dtk ) then
    setenv DTK_HOME /home/apps/dtk
  endif
endif
if ( $?DTK_HOME ) then
  setenv PATH "$PATH":"$DTK_HOME"
endif

reboot
login as nmrclass again
open a terminal and confirm that '/mnt/macmini' is the path to freesurfer and subjects dir
start testing tutorials, like qdec (Generate Data Tables, then load qdec.table.dat and run Analyze on age), and freeview