Whole-brain connectome using Schaefer parcellation

Welcome Lorenzo!

If the index values contained within a parcellation image are already incremental from 1 without any gaps, and you don’t wish to apply any kind of custom reordering / exclusion of nodes, then there is no need to apply the labelconvert step, since its core purpose—to produce a parcellation image where the contained values increment from 1 without any gaps—is already satisfied by the originating data. This appears to be the case for the Schaefer parcellation based on the contents of the provided LUT files, and also from my running the labelstats command on one of the parcellation images I chose at random.

If this is not the case if you generate the subject-specific parcellation image through FreeSurfer commands, then the labelconvert step may be required. But as I stated in a prior comment in the originating thread, unless somebody else has created such a file and is willing to share it, I am unsure how to formulate advice for the construction of such a file over and above the contents of the documentation page that would require less effort than just doing it myself.

Rob

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