Hi Bastian,
A few thoughts:
-
I haven’t played with
flirt
much myself, but it should be possible to apply the estimated rigid-body transformation to the header of the moving image only; effectively the ‘voxel grid’ of the moving image is translated & rotated, but the image intensities are unaffected. Subsequent resampling of the moving image onto the grid of the target image is not a compulsory component of affine registration, and should not be thought of as such. Indeed, it’s better to perform this registration but retain image volumes in their native resolution; many MRtrix3 capabilities are explicitly designed to properly handle multi-modal image data that are not on a common voxel grid.(From memory, this is achieved using
flirt -omat <flirt output>
, thenmrtransform -linear <flirt output> -flip 0
; anyone correct me if I got this wrong) -
Personally I have always registered T1 to (pre-processed) DWI before anatomical image processing (including before importing to FreeSurfer); that way, any images subsequently derived from the T1 should be inherently aligned to the DWI without requiring further explicit registration, and without necessitating manual tracking of which images are aligned and which are not.
-
Not that it should be necessary here, but since you brought it up: Any resampling of images with discrete values (e.g. aparc+aseg) should be performed with nearest-neighbour interpolation: this will maintain the labels from the input image during resampling, which is necessary in such contexts.
Cheers
Rob