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Download and Install FMRLAB

1. Download the following compressed files and save them in the same folder/directory (e.g., ~/matlab/fmrlab):

   • FMRLAB 4.0 (7.6 MB).

   • Binary ICA executable.

   • QuickStart tutorial (PDF format).

2. Download FSL

   • Download entire FSL package. You can learn how to download and install FSL package there.

   • Download only the routines needed for spatial normalization. You must read and acknowledge the FSL licenses before you download the normalization routines. Click here to view FSL license 1 and license 2.
     • I agree to the terms and conditions mentioned in the above two license pages (download Linux version).
     • I agree to the terms and condition mentioned in the above two license pages (download Mac OS X version).

3. Uncompress the downloaded FMRLAB files.

   % tar xvfz *.tgz

4. Download sample fMRI data set for tutorial and save it in another folder/directory (e.g., ~/fmri_data)

   • Compressed file (fmri_sample.tgz).

   • Uncompressed files ( 2dseq_r1, 2dseq_str).

5. Uncompress the tutorial data files

   % tar xvfz *.tgz

6. Add FMRLAB path to Matlab environment.

   To add FMRLAB path in Matlab, you can either:

   • Add absolute path where you installed FMRLAB to "~/matlab/startup.m" file.
     For example, open ~/matlab/startup.m file, add "path('/home/xxxx/matlab/fmrlab',path);" in the file you just opened.
     Or,

   • Launch Matlab, and type
     >> addpath('/home/xxxx/matlab/fmrlab'); everytime you want to start FMRLAB.

7. Set FMRLAB variables.

   • Edit fmrlab_icadefs.m file with any editor available. This file can be found under FMRLAB home directory.

   • Find variable ICADIR, change its content to the directory FMRLAB installed (say, "/home/xxxx/matlab/fmrlab/").

   • Find variable ICABINARY, change its content to "/home/xxxx/matlab/fmrlab/ica_linux".

   • Find variable SC, change its content to "/home/xxxx/matlab/fmrlab/binica.sc".

   • Be sure to make changes according to your environment properly.

8. Link FMRLAB to FSL spatial normalization program.

   • If you downloaded and install the entire FSL package: (learn how to install here)
     • Edit fmrlab_icadefs.m file with any editor available. This file can be found under FMRLAB home directory.
     • Find variable FSLDIR, change its content to the directory FSL package is installed.

   • If you only downloaded the spatial normalization routine:
     • Make bin/ subdirectory under FMRLAB home directory.
     • Copy the downloaded file, flirt_linux or flirt_mac to the bin/ directory just created, and rename it to flirt.
     • Edit fmrlab_icadefs.m file with any editor available. This file can be found under FMRLAB home directory.
     • Find variable FSLDIR, change its content to the FMRLAB home directory.

9. Now, you are ready to explore the FMRLAB.

Questions or comments to this page, please send e-meil to: fmrlab@sccn.ucsd.edu.