Structural coneectivity among ROIs

Dear MRtrix3 experts,

I have 10 brainstem ROI masks(.nii format in MNI space), and 16 subcortical regions resulting from freesurfer.
I have previously acquired the structural matrix file of HCP atlas, now I want to conduct the structural connectivity among these ROI regions, is there an easy way that tck2connectome to do it?

For my understanding, I have to firstly transform the .nii masks to each subject, know I’m struggling with the next steps: do I need to combine all ROIs into one .mif file?

Looking forward to your advice.


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Hi Sia,

Here’s something that might work if you just wanted to probe connectivity between the 10 brainstem and 16 subcortical ROIs (which have the same resolution)…

I think you will need a single mif file (let’s call it the parcellation image) containing all 26 regions, indexed from 1-26. This will result in a connectome matrix that has a size of 26x26 after using tck2connectome.

One way of generating this parcellation image is to extract each ROI as a separate binary mask (see mrcalc with -eq option), and reindex the binary mask with a unique value from 1 to 26 (using something like mrcalc <binary_mask> <index> -mult <re-indexed_mask.mif>).

Then add all the re-indexed masks together to get a parcellation image. This image should only contain values from 1-26.

It would be a good idea to ensure that the ROIs are indeed non-overlapping prior to adding (overlapping ROIs that sum together will result in mislabelled voxels at the boundary of overlapping masks…).

Hope this helps!