Hi FSL expert!
I'm trying to run a tractography from a specific seed mask to a target mask. To do so, I choose my seed then I used the target mask as a waypoint and termination mask. To have the connectivity matrix I also added the --omatrix2 flag but I'm a little bit confused about the space in which the target2 mask has to be. I run the tractography in the subject's native space (Freesurfer preprocessing) and provided the matrices of the transformations for the diffusion space but can the target2 mask be in this same native space? Or it needs to necessarily be in diffusion space (as suggested in the Fdt GUI)?
Thanks,
Sara
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