FreeSurfer/FSL Course Setup

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

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 the 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.txt 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 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 'fsfsl_cshrc' file whose contents are this:

setenv FREESURFER_HOME /usr/local/freesurfer
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 the FsTutorial dir 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 may 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 location, dates and lecturer names on the index page to match the new course.


  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.
  4. dont do any edits though as we want the data to be clean.


  1. create a tarball of the freesurfer directory (from the fsfsl_course course dir so that 'freesurfer' is included in the path) and send them the tarball to install into /usr/local.

  2. make sure the FSL guys:
    • run: chmod -R a+rwX /usr/local/freesurfer/subjects

    • add this line to the .cshrc file in the freesurfer account: source /usr/local/freesurfer/fsfsl_cshrc

    • setup Firefox on the 'freesurfer' account so that its default home page is /usr/local/freesurfer/FsTutorial/index.html and create an icon for Firefox on the desktop.

    • put a Terminal on the desktop as an icon on the 'freesurfer' account, and set preferences to make the mouse over the window become the active window (not critical though, just the way we like things)
    • make sure each of the PPT slides on the home page open (on Centos6 using LibreOffice)

    • have someone run the tutorial (except no editing), making sure that at least tkmedit, tksurfer, and freeview opens and that qdec runs the group analysis (which tests RW of the data and exercises a bunch of freesurfer binaries).

FsFslCourseSetup (last edited 2014-09-03 12:57:42 by ZekeKaufman)