Mrtrix3 alternative for fslreorient2std?

#1

Is there an equivalent mrtrix3 command for fslreorient2std?

Thx,
Stefan

#2

Hi Stefan,

Not entirely sure, but you could try

mrtransform input.mif output.mif -identity

cheers,
Thibo

#3

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