I have been trying to convert an aparc+aseg parcellation image that has been brought to the Diffusion space, from a .mif to a .nii.gz image, for the purpose of extracting specific ROIs from this image to be used in tractography. I did perform the following steps:
- Register b0 to T1 using FSL’s flirt and save the inverse transform
- Convert the inverse transform to mrtrix format using transformconvert
- Apply this transform to the aparc+aseg image converted to .mif format using mrtransform to form nodes.mif - aparc+aseg image in .mif format and in diffusion space.
Everything worked fine and the registration gave really good results. However, when I convert the resulting nodes.mif image into a nifti file using mrconvert, the output (nodes.nii.gz) seems to be misaligned with the .mif image(Screenshots attached). Kindly suggest what could have gone wrong.