Which FOD file to use for TractSeg in subject space

[smeisler]

@Tanja

However, I’m not sure this is correct since the tutorial mentions at that step “Note that here we warp FOD images into template space without FOD reorientation, as reorientation will be performed in a separate subsequent step (after fixel segmentation)”. I understand this as the FODs being registered to template space correctly but having the original orientation, and that running TractSeg on these files would be wrong.

Correct.

I’d run TractSeg as normal in subject space and then warp the streamlines to template space with tcktransform — MRtrix3 3.0 documentation. This is preferred over warping FD/FC/FDC since the only thing you are manipulating are valueless streamlines, so no worry about data interpolation.

Best,
Steven