Freesurfer on ARC

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Freesurfer is a collection of neuroimaging software that can be used to process Magnetic Resonance Imaging files like DICOMs and NIFTIs. Detailed documentation can be found on the [[ https://surfer.nmr.mgh.harvard.edu/ | Freesurfer website]]

Most simple workflows that are scalable on ARC use recon-all to perform a reconstruction of the MRI image from the collection of slices. This is done by parallelizing over scans or subjects.

Freesurfer Singularity Containers

Freesurfer Sample Script

Single Scan Script

Multiple Scans Reconstruction in Parallel with a Job Array