Thanks Doug! Could you clarify what you mean by the registration already being in anat-to diffusion? The only thing I did was to run bbregister using B0 as the -mov image and saving the reg.lta. If I understood correctly the registration matrix should be diffusion-to-freesurfer, shouldn't it?

Now I ran lta_convert --inlta reg.lta --invert --outfsl freesurfer-to-diff.mat. I believe freesurfer-to-diff encodes the transformation from freesurfer space to diffusion space, is that correct?

Best regards,

Sam

On Tue, Jul 23, 2019 at 3:15 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

Use lta_convert with --invert. BTW, the registration matrix is already anat-to-diffusion

On 7/22/2019 7:50 PM, Sam W. wrote:
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Thanks Doug! I'll use lta then, but which tool do you recommend I use for inverting the matrix in order to have a freesurfer-to-diffusion registration matrix? bbregister does not seem to offer the option to invert matrices. Is tkregister2 the preferable tool to use here? I realize there is an --lta-inv ltafile option. Would this be correct?:

tkregister2 --mov B0.nii.gz --fstarg --fslregout fsl.mat --s sub01 --lta-inv reg.lta

I'd like to output an FSL-style registration matrix because I intend to use some of FSL tools.

Thanks for your help!

Sam

On Mon, Jul 22, 2019 at 10:35 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

In most of the tools there is an option to invert the matrix before you
apply it. If you save the registration matrix as an LTA instead of DAT,
then most of the tools will figure out the directionality.

On 7/22/19 4:24 PM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hi,
> I would like to create a registration matrix from orig.mgz to
> diffusion space. I created a reg file with
>
> bbregister --t2 --init-fsl --reg /data/FS/sub01/reg.dat --mov
> /data/FS/sub01/B0.nii.gz --s sub001
>
> but how can I invert this registration so that the transformation goes
> from freesurfer to diffusion space?
> Thanks!
> Sam
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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