I’m running QSIprep (0.16.1) and fMRIprep (22.1.1) for a cohort of subjects, but I’m only running FreeSurfer inside fMRIprep. If my understanding is correct, the output from FreeSurfer should be already aligned with the T1w of QSIprep right? If then I want to align this output with the dwi, I just need to apply the transformation from the T1w to the dwi, right? thanks in advance.
No, the T1/DWI images output by QSIPrep are rotated to be ACPC aligned, so they will not be aligned with FreeSurfer outputs. Part of the HSVS reconstruction pipelines involves calculating the registration between FreeSurfer space and DWI space.