[http://marsbar.sourceforge.net MarsBaR] is a region of interest toolbox for SPM99, SPM2 and SPM5. It is installed at the CBU.
The development version supports SPM5. To use this, start SPM / matlab on a machine that will run SPM5 (see [:CbuComputingResources#Software:the CBU computing page]).
MarsBaR should be available via the toolboxes button (let MatthewBrett know if not).
You can also make MarsBaR available by manually adding the path:
To do this, type the following at the matlab prompt:
addpath /imaging/local/spm/marsbar/marsbar-devel-0.41 marsbar
to start MarsBaR.
Local help for MarsBaR
Some pages showing basic steps (with screenshots) exist.
[http://www.mrc-cbu.cam.ac.uk/people/jessica.grahn/marsbarcreateroi.html Steps for creating ROIs from an SPM cluster, and exporting ROIs to nii or hdr/img.]
[http://www.mrc-cbu.cam.ac.uk/people/jessica.grahn/marsbar.html Steps for extracting signal from Regions of Interest, for import into Excel/SPSS/etc., to do second level analysis.]
Here are some marsbar batch files: attachment:marsbarbatch.m : this batch file takes a list of coordinates and makes sphere ROIs, saving them in MarsBar and .nii format.
attachment:marsbarbatchextract.m : this batch takes all rois in a directory, and extracts data from all the con/beta images in another directory, saving the data to a text file.
attachment:marsbarbatchconvert.m : this batch file converts rois to .nii format