Local connectivity with MRtrix

Dear MRtrix experts,

I would need you help, I am trying to understand if there is any way to determine structural local connectivity (i.e. connectivity in smaller portions than the regions parcellated) from the ACT performed with MRtrix.



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Hi Mic,

As an example, let’s say the standard MRtrix3 DK parcellation image is being considered (indexed from 1 to 84). And let’s use the thalamus (indexed at 36 and 43) in this example (i.e., the goal is to replace the existing thalamus ROI with several smaller thalamus subfields).

For simplicity, let’s also assume that the sum of the subfields completely make up the original thalamus segmentation, and that the thalamus boundary in the 5TT image is the same as the boundary in the parcellation image. Additional steps might be required if these assumptions aren’t met…

Briefly, start by removing the existing thalamus ROIs from the parcellation image (to create a parcellation image that does not contain left and right thalamus). Then, reindex the thalamus subfield masks with unique integers (starting from 85 to N). Finally, add the re-indexed subfields to the parcellation image that does not contain the thalamus.

The result should be a parcellation image with integers from 1 to N that does not contain values 36 or 43 (since these were removed).

To consider the connectivity between subfields, consideration should also be given to how the underlying structure is labelled in the 5TT image used for ACT.

Here’s what our group have previously done, although we were working with the hippocampus GitHub - Marshall-Dalton/Pipeline_for_anatomical_connectivity_along_the_anterior-posterior_axis_of_the_human_hippocampus: This repository contains code for the following paper; Dalton et al., 2022. "Anatomical connectivity along the anterior-posterior axis of the human hippocampus: new insights using quantitative fibre-tracking." bioRxiv

Hope this helps!