Hi Andras,
I have a follow-up question here. My workflow currently crops the volumes with ROIs aligned to the RAS axes, computes the ACPC transform, and then resamples the cropped volumes. I noticed that an offset (arrow in the image below) is introduced between the coronal and sagittal volumes after the transformation. Could you please help explain this? I have already tried specifying the AC as rotation point in the rigid/affine parameters section of the resample scalar/vector/dwi volume - the offset is still visible.
Strangely, this is the case with only some of the scans I have.
I also noticed that if I apply the ACPC transform first, from the transforms module, harden it, and then crop the volumes, this issue does not arise.
Thanks!