MSM_HOCR: Multimodal Surface Matching with Higher Order Discrete Optimisation
This the version of MSM used in the HCP “A multi-modal parcellation of human cerebral cortex ” and is …
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(For research users only)
The packages also include few support binaries which should be all explained on the fslwiki (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/msm), and a sample config file for cortical folding based alignment, which although not recently optimised should be good to start with. For data other than cortical folding (such as functional maps), my experience is that you need to reduce the lambda parameters in the config files.