Warping functional ROIs from MNI space to wmFOD template space

[maxpietsch]

Hi Alex,

@Alex_Sphyrna

My understanding is that the FODs are already warped given that the underlying image, the DWI b=0, is already warped, but I’m not sure.

To calculate FODs you’d need more than the b=0 signal so I am assuming that you used the dMRI data to extract the b=0 image and to calculate the FODs. If your FOD image was generated from the image that contained the b=0 image, it would share the same space. Hence you’d need to apply the same warp to bring it to MNI space as was used to bring the b=0 image to that space.
Note that nonlinear transformations of raw dMRI data results in artefacted data, do not warp the dMRI data and calculate the FODs in the new space, rather calculate the FODs in dMRI native space and warp the FODs with appropriate reorientation (mrtransform -reorient_fod yes).

@Alex_Sphyrna

Do I need a new processing step to modify the FODs regarding the identity warp ?

You don’t need to recreate the warp as it contains the mapping from one space to another and is not tied to a particular image; it can be applied to either image.

@Alex_Sphyrna

I don’t have a deep understanding of this warp and transformation functions.

The wiki entry Registration, transformation, regridding: concepts might help.

Cheers,
Max