Is there an equivalent mrtrix3 command for fslreorient2std?
Thx,
Stefan
Is there an equivalent mrtrix3 command for fslreorient2std?
Thx,
Stefan
Hi Stefan,
Not entirely sure, but you could try
mrtransform input.mif output.mif -identity
cheers,
Thibo
If you’re after resetting the orientation of the image axes to RAS+ (the NIfTI standard frame), while preserving the image anatomical orientation, then in MRtrix-speak you’ll want to reset the strides – which you can do with a simple mrconvert
call:
mrconvert input.mif -strides 1,2,3 output.mif
(the example is for .mif
images, but this works for all supported image formats, including NIfTI).
I should also add that if you’re applying this on NIfTI DWI data with associated bvecs/bvals, it is essential that you also apply the corresponding modifications to the bvecs. To do this is a bit cumbersome – one of the reasons we advocate the use of the .mif
format:
mrconvert input.nii -fslgrad bvecs bvals -strides 1,2,3 output.mif -export_grad_fsl bvecs_out bvals_out