FSL WITH OTHER SOFTWARE


FreeSurfer - Cortical flattening and modelling

FreeSurfer is a set of semi-automated tools for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface, produced at MGH, Boston. We have worked together to make interoperation of the two packages as easy as possible.

AFNI - Freeware display and analysis

AFNI is a package for processing, analyzing, and displaying FMRI data. One of AFNI's particular strengths is that it is a powerful display tool. Recent changes to AFNI make it very easy to view FSL output, in particular, FEAT output.

MEDx - Commercial display and analysis

MEDx is a GUI-driven commercial image analysis and display package, available from Sensor Systems. The latest version of MEDx (3.4) comes with FSL release 1.2a built in. Alternatively, you can easily configure MEDx to seamlessly access the GUIs that come with the latest version of FSL: Set environment variable FSLDIR to the full path name of the top level FSL directory (fsl). You also need to install a few files into the standard MEDx distribution: see file fsl/etc/medx_customisation/README. If you integrate this release of FSL into MEDx (to take advantage of newer FSL features) then this will not interfere with the bundled older version of FSL. The bundled FSL is accessed through the MEDx Toolbox whilst this version will appear on the main (small) MEDx window.