I’m trying to change my .nii file to mif using
mrconvert *.nii -fslgrad *.bvec *.bval test.mif
[WARNING] qform and sform are inconsistent in NIfTI image “*.nii” - using sform
I think that warning is serious problem for pre-process diffusion image.
Do I input command wrong or missing something? and
if I use mrconvert *.nii -fslgrad *.bvec *.bval -json_import *.json test.mif
Is that right to input the json file on .mif file for dwifslprerpoc?
Your command is right. You get this warning because the nifti image you are using contains a contradicting qform and sform. You can find more info on this here: NIfTI transform ambiguity
Not necessarily, it could just be a very subtle mismatch due to machine precision – see this thread for details.
However, if there is a genuine mismatch, it might be worth chasing down where this mismatch originates, and which of the sform or qform is to be trusted…
If you have it, yes – though that has no influence on the warning you get. It just means that any additional information present in the JSON will also be injected into the header of the
mif file. You’ll basically end up with a single
mif file that contains all the voxel data, the bvecs/bvals, and any other information present in the JSON.
Thank you for your comment!