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Okay - thank you so much! I believe I understand. Using the linear transformation outputted by FLIRT (diff2standard.mat), run FNIRT. So the command for diffusion --> standard would be something like this:

fnirt --ref=/usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --in=nodif_brain.nii.gz --aff=xfms/diff2standard.mat --cout=fnirted_dwi_brain

And the invwarp command would be something like this:

invwarp --ref=nodif_brain.nii.gz  --warp=fnirted_dwi_brain --out=standard_to_dwi
And then applywarp?

Thanks,
Matt

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