Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.
This seems to require a full MATLAB installation to run (with Image Processing Toolbox installed). I think we should implement a capability to specify which resource the App should run on for pipeline. If we do, then we can inject MATLAB installation from the local cluster into the singularity container to run localGI, I believe.
Another alternative is to create a separate App (like app-freesurfer-localGI?) which will do above without user needing to specify resource with MATLAB installation - but it will basically duplicate freesurfer output.
Just noting things that I've found so far.
A few users have requested capability to run localGI (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI)
This seems to require a full MATLAB installation to run (with Image Processing Toolbox installed). I think we should implement a capability to specify which resource the App should run on for pipeline. If we do, then we can inject MATLAB installation from the local cluster into the singularity container to run localGI, I believe.
Another alternative is to create a separate App (like app-freesurfer-localGI?) which will do above without user needing to specify resource with MATLAB installation - but it will basically duplicate freesurfer output.