MarsBaR region of interest toolbox for SPM

MarsBaR (MARSeille Boîte À Région d'Intérêt) is a toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.

Reference

We presented an abstract to the Human Brain Mapping conference for 2002; this may be useful as a reference: Region of interest analysis using an SPM toolbox. It should apparently be cited as:

Matthew Brett, Jean-Luc Anton, Romain Valabregue, Jean-Baptiste Poline. Region of interest analysis using an SPM toolbox [abstract] Presented at the 8th International Conference on Functional Mapping of the Human Brain, June 2-6, 2002, Sendai, Japan. Available on CD-ROM in NeuroImage, Vol 16, No 2.

MarsBaR versions

MarsBaR releases come in two flavours: stable and development. As the names imply, the development versions will usually be more recent, and have more bugs. If you are starting with MarsBaR, start with the stable version.

The current stable version is 0.41. 0.41 works with SPM99, SPM2 and SPM5.

Download and install

All MarsBaR releases are available via the MarsBaR project download page. For the current stable release, look for the marsbar package; marsbar-devel is the development release. Releases consist of an archive which will unpack in a directory named after the MarsBaR version - for example "marsbar-0.41". You then have two options for using MarsBaR within SPM.

You can add the new MarsBaR directory to your matlab path. To use MarsBaR, start it from the matlab prompt with the command "marsbar", or...
You could set up MarsBaR to run as an SPM toolbox. To do this, the contents of the new MarsBaR directory needs to be in a subdirectory "marsbar" of the SPM toolbox directory.
Here is a worked example for Unix. Imagine SPM2 was in "/usr/local/spm/spm2", and you had just unpacked the MarsBaR distribution, giving you a directory "/home/myhome/marsbar-0.41". You could then create the marsbar SPM toolbox directory with:
```
      mkdir /usr/local/spm/spm2/toolbox/marsbar
      
```
and copy the MarsBaR distribution into this directory with:
```
      cp -r /home/myhome/marsbar-0.41/* /usr/local/spm/spm2/toolbox/marsbar
      
```
Alternatively, you could do the same job by making a symbolic link between the directories with something like:
```
      ln -s /home/myhome/marsbar-0.41 /usr/local/spm/spm2/toolbox/marsbar
      
```

Either way, the next time you start spm you should be able to start the toolbox by selecting 'marsbar' from the toolbox button on the SPM interface.

For those who need the very very latest code and edits, there is also a SourceForge MarsBaR SVN interface, and instructions for using anonymous SVN from the command line.

For writing credits and some little jokes, see the marsbar.m file in the MarsBaR release.

Documentation and help

Try the MarsBaR tutorial for an introduction to the interface:

MarsBaR tutorial in OpenOffice format

MarsBaR tutorial in PDF format

There is a separate tutorial for the development version:

MarsBaR-devel tutorial in OpenOffice format

MarsBaR-devel tutorial in PDF format

There is also a MarsBaR FAQ.

The MarsBaR code is reasonably well documented; we export this documentation as web pages using Guillaume Flandin's excellent m2html. This is available in the doc subdirectory in the main marsbar directory for the devel and stable versions. It is also available in the doc-stable/latest directory of the website, for the stable version, and the doc-devel/latest for the development version.

We hope it is clear how to use MarsBaR, but please let us know if you have problems. In particular, we would be very glad to hear of any bugs or inconsistencies.

There is a mailing list for MarsBaR; list archives and instructions for posting are available via the MarsBaR users mailing list page. There is also a MarsBaR mailing list archive. Gmane also provides a nice interface to more recent MarsBaR emails.

Thanks,

The MarsBaR team

Last Refreshed: Thu Jul 3 00:11:28 BST 2008