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Hi Ana, have a look here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Options_Tab for the different matrix options that you can choose when using Probtrackx2. If you are trying to get a structural connectome, you can use the matrix1 option (i.e., gray matter seeds to gray matter seeds). Once you have your “dense” connectome, you can parcellate it using any atlas you have available. If you want a ROI to ROI connectivity matrix, you can use the --network option in PBX2 after specifying your list of seed regions as input. In both cases, you can use either volumes or surfaces to define your seed regions. For more information on how to generate connectomes, have a look at the HCP course material: https://wustl.app.box.com/s/rd4q23kigh11kdrj0ndj9jip1tjk7id6 Hope this helps, cheers, Matteo On 23 Feb 2018, at 11:38, Ana Coelho <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL users, I would like to construct a voxel by voxel structural connectivity matrix of the whole brain. I don't know which of the following is the best option to do this in probtrackx: - input AAL ROIs as seeds with -matrix1 option and then fdt_matrix1 will be my voxel-wise connectivity matrix - input AAL ROIs as seeds and GW/WM boundary as termination masks with -matrix3 option Or maybe there is an alternative option that is better than these two. Thanks in advance, Ana