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:

1. find a shareable location to which LCN people can write files, or use this dir: /autofs/space/terrier_001/scratch/fsfsl_course

2. install freesurfer here, use a public tarball, which you can untar from here: /space/freesurfer/build/pub-releases

3. copy a .license file into the freesurfer dir

4. 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

5. make the data writable: chmod -R a+rwX freesurfer/subjects

6. from a CentosOS 6 64b machine, do this: cp -r /usr/lib64/GLoverride freesurfer 

7. 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

1. create a wiki snapshot from scratch (see SnapShotNotes) or just get a prior one from /cluster/pubftp/docs, for instance the FsTutorial-Auckland2012.tgz tarball and untar it to: freesurfer which should create a dir named FsTutorial

2. copy all the slides to the docs directory that is underneath the FsTutorial directory

3. edit the index.html page in FsTutorial so that the slide links point at those in the local freesurfer/FsTutorial/docs directory. note that if you are using a prior snapshot, and the course is the same, the index.html make already correctly point at the slides (but very likely new slides need to be copied to docs. also if you used a prior snapshot, be sure to update the dates on the index page to match the new course.

4. make sure the FSL guys setup Firefox so that its default home page is /usr/local/freesurfer/FsTutorial/index.html and create an icon for Firefox on the desktop.

5. make sure the FSL guys put a Terminal on the desktop as an icon, and set preferences to make the window over the mouse become the active window (not critical though, just the way we like things)

testing

1. unplug the machine from the network to simulate a local machine as found in the course (or as root type server network stop)
2. point your browser at the Fstutorial/index.html file
3. click through the entire tutorial, making sure each slide opens, and each tutorial command executes. be certain that tkmedit, tksurfer, freeview and qdec all work, and make sure that whoever is doing the testing on the FSL image machine does the same.