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).

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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