I will be doing an analysis that requires functional and tractography data to be in native space or some rigid transform thereof (so any common space that does not require affine spatial normalization such as MNI). QSIPrep ACPC aligns data, so outputs are rotated compared to fMRIPrep’s. Since tractography derivatives are the largest, I probably want to align functional data to DWI to limit computational needs, and I imagine using the T1s is the best way to go about this. However, since neither of the output T1s in
anat are skull stripped, a simple
flirt will has not sufficed. Anyone have suggestions for getting the most reliable transform between subject-space outputs of the two softwares? Should I just skull trip the two images and then try to align? Can I make use out of knowing how both images are transformed to MNI? Thanks in advance!