Describe FsTutorial/CourseSetup_easy here.
FreeSurfer Course Setup
Notes on how to do the physical setup of the computers and stuff for the course. Also see FreesurferCourseAdminNotes
Contents
Laptop Hardware
Laptop hardware should meet or exceed the recommended System Requirements for running freesurfer.
- In addition to the listed System Requirements, laptops should have 17" screens to facilitate viewing of images on the screen.
- Laptops should have internet access. (For following course tutorials and performing last minute updates of the data set)
Laptop Software
Laptops should have the "Development Version" of freesurfer installed either locally, or via a central server.
Optional: If the course is doing the Diffusion tutorial, than laptops should have FSL installed.
Optional: If the course is doing the FSFAST tutorial, than laptops should have the Matlab runtime installed (version 8.3, no license required). However, the commands requiring Matlab have been marked and can be skipped because the output data has already been provided. So Matlab is not an absolute requirement.
Tutorial Data
Laptops should have access to the "Lightweight" version of freesurfer tutorial data either downloaded locally, or via a central server, or external storage device (thumb drive, external hard drive, etc). Note that it is important for each laptop to have access its own sandboxed version of the data, with read/write access, because course participants will be creating files within their workspace.
Startup Script
The following lines should be added to a .bashrc file in the users home directory so that freesurfer is automatically sourced (and other environment variable set) whenever a terminal window is opened.
## Set location of tutorial location export TUTORIAL_DATA=<location_of_tutorial_data> ## Set location of FSL (Required for Diffusion tutorial only) export FSLDIR=<location_of_fsl_installation> ## Set location of Matlab and other variable (Required for FSFAST tutorial only) export FS_MCRROOT=<location_of_matlab_installation> export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/runtime/glnxa64" export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/bin/glnxa64" export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/sys/os/glnxa64" export FS_SPMREG_USE_BIN=1 export FS_MKCON_USE_BIN=1 export FS_SXA3_USE_BIN=1 ## Source freesurfer export FREESURFER_HOME=<location_of_freesurfer_installation> source $FREESURFER_HOME/SetUpFreeSurfer.sh
Testing
Once the steps above have been taken, the best an most reliable way to test your setup is simply to run thru one or more of the many freesurfer tutorials.
A more automated way to test your setup is to run the test_tutorials.sh script. This script comes with freesurfer and can be run in the following ways:
$> <source_freesurfer> # Display help $> test_tutorials.sh --help # Run a quick test $> test_tutorials.sh -