Many MRI steps only work if the scans are roughly aligned with the MNI template. Rotations (pitch) in particular is difficult to compensate for.
Sep 2020 Onwards
T1 Legacy
Gets manually aligned in project folder Manually Aligning T1's to MNI
All scans
Determine manual coregistration parameters, and automatically apply.
All MRI studies can have a coregistration from the original nifti (as converted in CSPM) to overlap MNI space. The parameters are determined for each scan, although these can be copied across scans and studies.
The question is: are the coregistration parameters applied in “rawimages” or in the “…preprocess” folders?
Example of new GUI
Up to Sep 2020
T1
Gets manually aligned in project folder Manually Aligning T1's to MNI
Failed experiment:
All other scans get T1 coreg parameters applied
Rationale was that person in scanner would have similar orientation for all scans (e.g, 30 degree pitch for T1, fMRI, DTI, etc.). This is actually not the case genreally, as various scans have various orientations, and it was only a conincidence when fMRI and T1 rotations were the same. This is now basically disabled in CSPM unless you go through several hoops.
Non-T1 scans:
Manually adjust in project rawimages nifti folders