Beginner: Connectome pipeline (Updated)

I have very good experience on skull-stripping in structural data with PreFreeSurfer HCP pipeline:


You can switch off gradient nonlinearity correction or readout distortion correction of structural images if you do not want to (or do not have required additional data for that).

Hi Elijah,

Thanks for the pipeline you’ve presented here. It’s actually a nice and well-described pipeline. I have a question. Is there something that you didn’t use the SIFT output as the tck2connectome input here?

tck2connectome i.tck i_nodes.mif i_connectome.csv -zero_diagonal

i.tck is the tckgen output, i_sift.tck is the SIFT’s.

Bests,
Amir