Using manual ROIs in the human connectome dataset

Hi everyone,

I am using MRtrix to reconstruct a tract from the HCP dataset. I already tried a single subject and everything works well. The problem is that the tract requires specific manual ROIs. Drawing those for 900 subjects doesn’t make sense. Does anybody know of a way to transfer ROIs into each subject’s space with existing transformation matrices in HCP? I could either draw the ROIs in template space or use the ROIs I drew for the single subject to push them in the space of all the other subjects.

Any help is appreciated.


Never mind, got the answer from the HCP mailing list. The transforms are in $subject/MNINonLinear/xfms.

Allow me to ask one more question on this topic (not sure if someone asked this already). Can the flirt warps (in the xfms folder) be used to warp tracts in a common space, so that I can combine them all together and obtain an average density map from all the subjects. This is mostly for display purposes.