I have large set of data with dwi and t1 data already aligned.
However, they have wrong RAS scheme as seen on the picture.
I have noticed that if I change the scheme from RAI (as it is present) to LSP the orientation corrects.
The same thing is if i do -axes 0,2,1 with mrconvert
However, since there is a difference in dimension of the image and voxel sizes, t1 and dwi are not aligned anymore after that.
Is there a possibility to get a proper orientation without losing the alingement of t1 and dwi?
I have tried reorienting both images and then coregistration of t1 to dwi, but it is not aligned that well as it is on the begining.