Dear Stefano,
> how can I do to co-registate with FNIRT on a common template the
> single maps of MD and RD of each subject?
>
> For FA I do:
>
> flirt -ref /usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz -in dti_FA.nii.gz -omat my_affine_transf.mat
> fnirt --in=dti_FA --aff=my_affine_transf.mat --
> cout=my_nonlinear_transf --config=FA_2_FMRIB58_1mm
> applywarp --ref=/usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz --in=dti_FA.nii.gz --warp=my_nonlinear_transf
> --out=my_warped_FA
>
> If I repeat these operations or only the last line foe MD and RD:
>
> flirt -ref /usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz -in dti_MD.nii.gz -omat my_affine_transf.mat
> fnirt --in=dti_MD --aff=my_affine_transf.mat --
> cout=my_nonlinear_transf --config=FA_2_FMRIB58_1mm
> applywarp --ref=/usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz --in=dti_MD.nii.gz --warp=my_nonlinear_transf
> --out=my_warped_MD
>
>
> flirt -ref /usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz -in dti_RD.nii.gz -omat my_affine_transf.mat
> fnirt --in=dti_RD --aff=my_affine_transf.mat --
> cout=my_nonlinear_transf --config=FA_2_FMRIB58_1mm
> applywarp --ref=/usr/share/data/fsl-mni152-templates/
> FMRIB58_FA_1mm.nii.gz --in=dti_RD.nii.gz --warp=my_nonlinear_transf
> --out=my_warped_RD
>
>
> my output generate a distorted map.
your problem is that you are still specifying an FA map as the target
for fnirt. If these are all from the same subject you should not need
to run fnirt multiple times. Run flirt+fnirt+applywarp for your FA
data, as you have done above and then apply those same warps to your
MD and RD data with calls to applywarp.
Good luck Jesper
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