Hi Mark,
Thanks for the response. We have tried registration of the FA map to the FMRIB58_FA template using FNIRT and the results do look better. However we are not sure how the Hardvard-Oxford's cortical ROIs line up with this space. They do not appear to align properly.
We have also tried FNIRT for co-registration of the DTI brain to the T1 brain without contrast brain with okay results (see code below). However we are still having the consistent problem of a larger output brain with all of our FNIRT attempts.
fnirt --ref=T1_brain.nii.gz --in=nodif_brain.nii.gz --inmask=nodif_brain_mask.nii.gz --refmask=T1_brain_mask.nii.gz --iout=dti2t1_fnirt.nii.gz --aff=dti2t1_flirt.mat --cout=dti2t1_fnirt_cout
…where we used both the affine transformation matrix (output of flirt) of the dti brian to the T1 brain and a BBR transformation matrix (output of FEAT) for the --aff input. Both yielding similar results.
If you have any other information that could help, please let us know.
Thank you,
Nicole
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