Using MRtrix3 I performed a tractography from all voxels in an ROI to cortical targets as defined by a parcellated image, all that in subject space.
The output is a 4D image that contains, at each voxel, the number of connections to each target, and now I need to normalize this latter image to MNI space.
I previously estimated deformation fields using SPM for a separate analysis, and I thought to simply apply the SPM deformation field to the image mentioned above (the “number of connections” image).
I heard that spatial normalisation of diffusion data is not recommended, especially before performing the tractography. However the latter is done already, and in my case I think that the connectome type of analysis is not an option : I want to look at connectivity profiles of voxels to cortical targets, and I need MNI coordinates comparable across subjects for all these voxels.
I could of course use SPM but the latter is not especially meant for diffusion data, and while MRtrix seems more appropriate I am new to it.
What procedure would you recommmend? Shall I use mrtransform, mrregister, or something else? What shall I use as interpolation options?
Many thanks for your help