Registering mask in FLAIR space to FBA template space

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Hi everyone,

I’d like to use a lesion mask that’s derived from FLAIR images in subject space on my FBA output to look at average FDC within the lesions and to also use CFE within the masked areas. I can’t seem to make the registration of FLAIR_subject to WMFOD_template work. I’ve tried/considered a couple options:

  1. Since I have the subject2template_warp.mif files, one option could be registering FLAIR_subject to WMFOD_subject (with FSL FLIRT since mrregister cannot be used between modalities) and then concatenating that transformation with subject2template_warp.mif and using it on the masks, but I don’t think that can work because the first transformation is a rigid one and I don’t think I can concatenate the resulting transformation matrix with a deformation field.

  2. I tried using FSL to do

FLAIR_subject  --FLIRT-->   WMFOD_subject
b0_subject     --FLIRT-->   WMFOD_template
b0_subject     --FNIRT-->   WMFOD_template

and then using the resulting deformation field on the masks, but the FNIRT step returned a NaN-filled deformation field which makes me suspect that normal images can’t be registered to FODs (at least not with FSL).

  1. I’m now considering the third option of using population_template on B0 images to create a B0 template which should be in the same space as the WM FODs, and then using that in my FLIRT + FNIRT option.
    I feel like I’m reinventing the wheel for a trivial problem, does anyone have a recommendation? Or is this not really trivial after all and will need some tricks to work?

Thank you in advance!