Bypass NIfTI conversion

[Lestropie]

I couldn't help noticing from a quick perusal of your code that converting from fixel data .mif files to HDF5 currently requires an intermediate conversion to NIfTI-2 via MRtrix3 mrconvert, such that the resulting .nii can be loaded using NiBabel.

It would be quite a lot more preferable if NiBabel could itself directly read .mif images.

I mentioned this in MRtrix3/mrtrix3#2087, and it was also mentioned over at NiBabel in nipy/nibabel#927. Unfortunately the intern I placed on the project wasn't able to finalise the contribution, but it might be possible to finish that code off and contribute it to NiBabel, which would likely be of use to many people but also would simplify the ConFixel code.

[mattcieslak]

@Lestropie that would be amazing! The nifti conversion is a big vulnerability here, as it sometimes flips the array of fixel values.

[Lestropie]

Yeah, that'll happen. Welcome to the wonderful world of image strides... 😬