Mrconvert issue

Hi MRtrix3 community,

Hopefully you can help !

I am trying to register wmfod_norm to T1 by registering bo to T1 and applying the transformation to wmfod_norm. First of all, I need to convert wmfod_norm.mif to nifti file to perform registration.

I used mrconvert to do it → mrconvert wmfod_norm.mif wmfod_norm.nii.gz.
Unfortunately, the orientation changed and I don’t seem to understand why or find the solution.

Thank you in advance for your assistance

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This is almost certainly related to the image strides. Try: mrconvert wmfod_norm.mif wmfod_norm.nii.gz -stride -1,2,3,4

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Thank you very much. It is working !