so I’m using nodes_fixSGM.mif file (output of labelsgmfix command) as -seed_image for my tractography (tckgen).
So you’re seeding exclusively from subcortical GM?
No; but also yes.
That’s the full parcellation image, which has been fed through
labelsgmfix, being provided as the seed image.
tckgen will interpret this as a binary mask when provided to
-seed_image. So it’s basically interpreted as a GM binary mask. The trouble with that if you are using ACT is that because FreeSurfer only labels cortical voxels in cases where the GM partial volume fraction is large (don’t know the exact logic used there), basically all streamline seeds drawn from within cortical voxels will be rejected as plausible streamline seeds, because they will have a GM > 0.5 partial volume fraction and therefore can’t be used as a seed, because
-seed_gmwmi was not used.
Should I edit
fs_a2009s.txt file based on my ROIs for
and the last question, the output matrix of tck2connectome command is 153*153 but fs_a2009s contain 165 ROI. Is something wrong with my output?
The only reason why you would potentially need to use an edited version of that file is if you want your connectome construction to deviate from the provided file in some way; e.g. changing the order of nodes, or excluding nodes, or the like.
If the output of
tck2connectome gives a different number of rows / columns than what is expected, then that is an issue with your data or processing that needs to be diagnosed; it’s not simply a matter of editing the lookup table file, as there’s no understanding of what modification would even need to be done. I can only suggest manually inspecting the outputs of your various processing steps and trying to diagnose the first point at which the data deviates from what you expected.