T1-MRI Segmentation with SPM12 / CAT12

Authors: Francois Tadel

CAT is a SPM12 toolbox that is fully interfaced with Brainstorm. It can replace efficiently FreeSurfer for generating the cortical surface from any T1 MRI. It runs on any OS in about 1 hour, instead of the typical 24hr FreeSurfer recon-all processing. The surfaces are registered to the templates with the FreeSurfer spheres, and include many anatomical and functional atlases.

You can either run the CAT segmentation from Brainstorm, or run it separately and import its outputs as you would do with FreeSurfer. The software is not packaged with Brainstorm and does not work with the compiled version of Brainstorm, you must install SPM12 and CAT separately.

Install SPM12

• Download SPM12: https://www.fil.ion.ucl.ac.uk/spm/software/download/

• Unzip it anywhere on your computer, but not in any of the Brainstorm folder.

• Do not add the spm12 folder to your path if you are not a SPM user, Brainstorm will do this automatically when needed.

• Start Brainstorm, set the SPM12 path in the Brainstorm preferences (File > Edit preferences).

Install CAT12

• Download CAT: http://www.neuro.uni-jena.de/cat/index.html#DOWNLOAD

• Unzip the downloaded file.

• Move the cat12 folder to the spm12/toolbox directory

Running CAT from Brainstorm