Hi,
I would like to register a FreeSurfer segmentation (or actually the corresponding T1 image) to another scan of the same subject. In order to perform this registration, the mri/T1.mgz file needs to have the same orientation as the original T1 scan (mri/orig/001.mgz). Resampling is not necessary since I want to prevent multiple interpolations and resampling is already necessary in the registration/transformation.
How can I convert mri/T1.mgz to the same orientation as the original T1 scan?
Thanks! Renske