Anastasia would know better but she is away for a week or two. But 
looking at it, I would say that your command line is correct. The 
registration does map the anat to the diffusion space, but mri_vol2vol 
understands this and simply inverts the matrix. You should just verify 
it for yourself by looking at the output. This has caused confusion for 
a long time ...

On 07/14/2015 02:05 PM, Celine Louapre wrote:
> Hi Freesurfer experts
> I am always a little confused with the registration matrices from tracula
> output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon
> space, do we use the matrix anatorig2diff.bbr.dat?
>
> mri_vol2vol --mov /<recon>/dmri/dtifit_MD.nii.gz --targ
> /<recon>/mri/brainmask.mgz --reg /<recon>/dmri/xfms/anatorig2diff.bbr.dat
> --o <recon>/mri/dtifit_MD_registered.nii.gz
>
> Thanks a lot
> Celine
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>
>

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MGH-NMR Center
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