Vertex-wise structure connectome

1

Hi all,
I am attempting to construct a connectivity matrix in which each node is a vertex of a freesurfer surface. Is there a way that I can create a labelled parcellation image in which each node refers to a specific point in on the freesurfer surface and use this in tck2connectome?

Thanks so much!

2

Dunno if its feasible.
But take into account that this would result into a matrix of 336000 x 336000. Depending on how this is done it wont be very… computationally feasible. You could use a downsampled fsaverage space.

This being said… I am not sure if it does make sense tu use each vertex as a node, given that DWI data comes from a lower-resolution and you will have smoothness and, as a result, redundant info there…

Anyway, I am not familiar with tck2connectome nor if it accepts surface images. However, if your goal is to create a dummy/fake parcellation, I would load the surface using python/matlab, and generate a fake parcellation with numbers going from 1-330k and save it as .annot.
This should do the trick.

3

Probtrackx2 can use surface GIFTI inputs.