I recently ran the QSIPrep Recon pipeline and wanted to use the output connectivity matrix, however I noticed that some matrices have bigger dimensions than nodes. From what I understand, the matrix should be n nodes x n nodes however mine all seem to be bigger. For example, Gordon333 is 385x385, Brainettome264 is 256x256. What could be the problem?
How are the atlas regions numbered in the atlas file you’re using? MRtrix3 prefers them to be numbered 1-n (e.g., 1-246 for Brainettome) but sometimes atlas files are provided without this convention (e.g., the HCP MMP atlas goes from 1-180, 201-380, etc.). If this is indeed the case, you can use
labelconvert to make a new atlas file with the old file, old lookup table, and new lookup table (see documentation here).