FreeSurfer/Fsl Course Setup

Notes on how to prepare a freesurfer bundle used for the yearly FSL/Freesurfer course. Some general notes:

Course machines do not have an internet connection.
This means all binaries, data, slides and wiki pages must be local.
The FSL guys do all the machine preparation: get machines that run CentosOS and have a suitable graphics card with at least 30GB of space for our stuff. They also create a 'freesurfer' account for use defaulting to csh.
Everything needed for a course will be found in the /usr/local/freesurfer directory, and that is the bundle we are about to create....

freesurfer bundle

All binaries, data, slides and static wiki pages need to be assembled into one directory, tarballed, and sent to the FSL guys to put on their image machine. These are steps to assemble this bundle locally:

find a shareable location to which LCN people can write files, or use this dir: /autofs/space/terrier_001/scratch/fsfsl_course
install freesurfer here, use a public tarball, which you can untar from here: /space/freesurfer/build/pub-releases
copy a .license file into the freesurfer dir
determine which tutorial data will be used for the course and put it under the freesurfer/subjects dir, typically this means to copy this dir: /space/freesurfer/subjects/buckner_data but note that its better to create a tar first then untar, since you dont want to copy the data in the symlinks, just the symlinks, or just use this tarball: /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/ buckner_data-tutorial_subjs.tar.gz
make the data writable: chmod -R a+rwX freesurfer/subjects
create a slides directory and copy all the slides into that dir
from a CentosOS 6 64b machine, do this /cp -r /usr/lib64/GLoverride freesurfer/
create file called fsfsl_cshrc containing these lines, and in the .cshrc that the FSL guys create for us for the 'freesurfer' account it should source this file:

setenv FREESURFER_HOME /usr/local/freesurfer
setenv LD_LIBRARY_PATH $FREESURFER_HOME/GLoverride
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
source $FREESURFER_HOME/SetUpFreeSurfer.csh

create a wiki snapshot and copy it to: freesurfer/FsTutorial
edit the index.html page in FsTutorial so that the slide links point at those in the local freesurfer/slides directory
point your browser at that local index.html file
unplug the machine from the network and make sure it all slides and tutorials work
make sure the FSL guys setup Firefox so that its default home page is /usr/local/freesurfer/FsTutorial/index.html