I’m currently trying to use tckgen and tcksift output to create a connectome based on AAL atlas (I’m creating the conectome itself with a different tool).
The problem is that right now I get tracts with endpoints both within and outside the atlas regions, meaning the final connectome will have a varying amount of tracts, depending on how many were generated inside the mask.
I would like to be able to generate the tracts on a whole-brain basis, but then screen out only the ones that start and end inside a given mask so that I get sifted tracts that are all inside my connectome nodes.
I know I can do one of the folowing:
- use tckgen with the -seed_image option
seems like -seed_image affects the seeds but doesn’t help me with endpoints inside the mask. is there an option that lets me define both endpoints of the tract to be in a mask?
- use tckgen, then manually choose only the tracts with endpoints in the mask, and only then use tcksift for a set number of tracts.
I was wondering if there is a way to achieve this (a set number of sifted tracts with endpoints in a given mask) during the sift stage, and not during the tract generating stage.