Get Linux computer with Ubuntu (Linux computer specs )
Set up Ubuntu environment (Ubuntu basic software setup )
Map network drive (Linux map network drive )
Install Freesurfer following instructions (see https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and Freesurfer setup notes )
Install MATLAB (Notes on installing MATLAB)
Install FSL (see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation and FSL setup notes )
Do after MATLAB, as FSL installation modifies startup file
Install as root, probably to make fmriprep work (not sure if this is the right thing to do, 17 Aug 2023)
If “sudo python fslinstaller.py” does not work, try “sudo python3 fslinstaller.py”
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