ROI-based fixel-based analysis

[NicDC]

Hello,

There’s a few things to consider here:

1. The BNA is already in MNI152 space as far as I can tell, so you shouldn’t need to register it again
2. The reference for the wmfod_template to MNI step should be a T2-weighted MNI image, not a T1-weighted or label image as it is now
3. Don’t use nearest neighbor interpolation while calculating the transform and warp, only when applying it to move the label image (atlas) to the wmfod_template

Generally, to figure out where the registration is failing, overlay the output image with the reference image at each stage.

@hyting

And in case that I misunderstand, if the registration of Atlas to wmfod_template goes well, the next step would be use the command tcktransform to transform the tracks file which generated by tckgen from the wmfod_template to the MNI Atlas, do I understand that right?

Depends on what you want to do - I was giving you instructions on how to move the Atlas labels to the wmfod_template so that you could use the labels to build a connectome (using tck2connectome) and then select the tracks assigned to the thalamus nodes (using connectome2tck). I think this is what the authors of that paper did, but you could also approach it by warping the tracks to MNI space and then doing something similar - not sure whether one approach is better than the other.

Cheers,
Nick