Registration of SH data to structural data

1

Dear MRtrix community,

I have a question regarding to the new command mrregistration, is it possible to register the cSD file to the structural data? I know is a bit strange, but I would like to know how the registration handles the fOD in that case. Thanks in advance.

Regards,

Manuel

2

Hi Manuel,
No you cannot register a FOD image (4D) with a 3D image. However, you could rigidly register either the DWI mean b=0 image (dwiextract dwi.mif -bzero - | mrmath - mean b0.mif) or the first SH coefficient (mrconvert fod.mif -coord 3 0 -axes 0:2 dc_term.mif) to the anatomical image.

The only issue is that mrregister does not yet have an image metric that can handle different contrasts (such as mutual information). This is something we will add in the future. In the mean time, you could try something like FSL FLIRT or ANTS. Then convert the output transformation to a MRtrix format (using transformcalc) to apply this to a FOD image (if you require the FOD image in the space of the structural image).
Cheers,
Dave

3

Hi Dave,

Thanks for your answer.

I was thinking about this, and I have one doubt, if I rigid register the B0 to the T1w and after I apply the transformation to all the volumes, the voxel size changes (2x2x2 to 1x1x1). Taking into account the reorientation of the gradients, how this will affect later to the cSD?

Cheers,

Manuel

4

Hi Manuel,
If you really want the FOD images at the same resolution, you could always down sample the T1w image (with mrresize) to be the same resolution as the DWI before using it in the -template option of mrtransform. If you use piping you don’t even have to save this as an intermediate image.

Performing CSD on the higher resolution image will perform as expected. However, I guess it depends on what you plan to do with the FOD images afterwards. I typically work with up sampled data in a fixel-based analysis. However for tractography, changing the resolution will affect the default step size and therefore the output streamlines. For related posts see here and here.

Hope this helps,
Dave

5

Hi David,

Thanks, these comments are really useful.

Regards,

Manuel