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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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 CautionHi, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Use lta_convert with --invert. BTW, the registration matrix is already anat-to-diffusion
On 7/22/2019 7:50 PM, Sam W. wrote:
External Email - Use Caution
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.edumailto: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 CautionHi, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use CautionThanks 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 CautionHi, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The registration matrix maps an XYZ coordinate in the diffusion space to an XYZ coord in the anatomical space. This appears to be counter intuitive. In the end, the direction is not very important because you can just invert the matrix to go the other way. It only really becomes important if you are trying to write your own transform or trying to interpret the matrix in some way. As for your lta_convert command, you can look in the lta file to see what the source and targets are.
On 7/23/19 5:39 PM, Sam W. wrote:
External Email - Use Caution
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 mailto: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:External Email - Use Caution 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 <mailto: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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sam W.