TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same template.
AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the same template, so that I can then take slices of brainmask.mgz and the superimposed WM surface accross subjects and compare them, confident that they are well alligned.
WHAT I TRIED: used *mri_robust_register *to register all the brainmask.mgz images to a T1_1mm_template. I looked for the respective "surface" template to register the surfaces, and maybe use *mri_surf2surf*, cannot find a "surface" template that corresponds to the "T1" template. *Ideally I would like to use the same .lta transformation BOTH for the T1 image and the surface*. As I understand (?) they have a different mesh-transformation matrix.
Best regards, Paolo
Hi Paolo
if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course)
cheers Bruce
On Fri, 31 Mar 2017, Paolo wrote:
TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same tem plate. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the s ame template, so that I can then take slices of brainmask.mgz and the superi mposed WM surface accross subjects and compare them, confident that they are well alligned. WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz ima ges to a T1_1mm_template. I looked for the respective "surface" template to register the surfaces, and maybe use mri_surf2surf, cannot find a "surface" template that corresponds to the "T1" template. Ideally I would like to use the same .lta transformation BOTH for the T1 image and the surface. As I und erstand (?) they have a different mesh-transformation matrix. Best regards, Paolo
Thank you for your answer. I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $ <some_command> brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $ <some_command> lh.white lh_registered.white --apply_transf talairach.lta
I aim to do this an all subjects: will they be aligned between themselves after the process?
Thanks
2017-03-31 15:59 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Paolo
if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course)
cheers Bruce
On Fri, 31 Mar 2017, Paolo wrote:
TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same
tem
plate. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to
the s
ame template, so that I can then take slices of brainmask.mgz and the
superi
mposed WM surface accross subjects and compare them, confident that they
are
well alligned. WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz
ima
ges to a T1_1mm_template. I looked for the respective "surface" template
to
register the surfaces, and maybe use mri_surf2surf, cannot find a
"surface"
template that corresponds to the "T1" template. Ideally I would like to
use
the same .lta transformation BOTH for the T1 image and the surface. As I
und
erstand (?) they have a different mesh-transformation matrix. Best regards, Paolo
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for volumes you can use either
mri_convert -at <transform>
or
mri_vol2vol.
For surfaces I think mris_transform should do the trick (and possibly mri_surf2surf, but I defer to Doug on this)
Bruce On Fri, 31 Mar 2017, Paolo wrote:
Thank you for your answer. I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $ <some_command> brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $ <some_command> lh.white lh_registered.white --apply_transf talairach.lta
I aim to do this an all subjects: will they be aligned between themselves after the process?
Thanks
2017-03-31 15:59 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Paolo
if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course) cheers Bruce On Fri, 31 Mar 2017, Paolo wrote: > > TO: freesurfer@nmr.mgh.harvard.edu > SUBJECT: Registration of both the brain and the "surf" files to the same tem > plate. > AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the s > ame template, so that I can then take slices of brainmask.mgz and the superi > mposed WM surface accross subjects and compare them, confident that they are > well alligned. > WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz ima > ges to a T1_1mm_template. I looked for the respective "surface" template to > register the surfaces, and maybe use mri_surf2surf, cannot find a "surface" > template that corresponds to the "T1" template. Ideally I would like to use > the same .lta transformation BOTH for the T1 image and the surface. As I und > erstand (?) they have a different mesh-transformation matrix. > Best regards, > Paolo > >
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For further clarity, we want to evaluate the geometric distortions to test how robust different sequences are to the local magnetic filed/susceptibility variations. So we want to keep the image as untouched as possible, but possibly aligned for comparison.
Is there an option in FS to register an image with 7 DOF (global rescale)? I am thinking of* mri_robust_register,* for which I see 3, 6, 12 DOF (--transonly, default and --affine).
2017-03-31 19:59 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
for volumes you can use either
mri_convert -at <transform>
or
mri_vol2vol.
For surfaces I think mris_transform should do the trick (and possibly mri_surf2surf, but I defer to Doug on this)
Bruce On Fri, 31 Mar 2017, Paolo wrote:
Thank you for your answer.
I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $ <some_command> brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $ <some_command> lh.white lh_registered.white --apply_transf talairach.lta
I aim to do this an all subjects: will they be aligned between themselves after the process?
Thanks
2017-03-31 15:59 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Paolo
if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course) cheers Bruce On Fri, 31 Mar 2017, Paolo wrote: > > TO: freesurfer@nmr.mgh.harvard.edu > SUBJECT: Registration of both the brain and the "surf" files to the same tem > plate. > AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the s > ame template, so that I can then take slices of brainmask.mgz and the superi > mposed WM surface accross subjects and compare them, confident that they are > well alligned. > WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz ima > ges to a T1_1mm_template. I looked for the respective "surface" template to > register the surfaces, and maybe use mri_surf2surf, cannot find a "surface" > template that corresponds to the "T1" template. Ideally I would like to use > the same .lta transformation BOTH for the T1 image and the surface. As I und > erstand (?) they have a different mesh-transformation matrix. > Best regards, > Paolo > >
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you can try mri_coreg with --dof 7
On 4/4/17 2:31 AM, Paolo wrote:
For further clarity, we want to evaluate the geometric distortions to test how robust different sequences are to the local magnetic filed/susceptibility variations. So we want to keep the image as untouched as possible, but possibly aligned for comparison.
Is there an option in FS to register an image with 7 DOF (global rescale)? I am thinking of/mri_robust_register,/ for which I see 3, 6, 12 DOF (--transonly, default and --affine).
2017-03-31 19:59 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
for volumes you can use either mri_convert -at <transform> or mri_vol2vol. For surfaces I think mris_transform should do the trick (and possibly mri_surf2surf, but I defer to Doug on this) Bruce On Fri, 31 Mar 2017, Paolo wrote: Thank you for your answer. I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $ <some_command> brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $ <some_command> lh.white lh_registered.white --apply_transf talairach.lta I aim to do this an all subjects: will they be aligned between themselves after the process? Thanks 2017-03-31 15:59 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Paolo if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course) cheers Bruce On Fri, 31 Mar 2017, Paolo wrote: > > TO: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > SUBJECT: Registration of both the brain and the "surf" files to the same tem > plate. > AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the s > ame template, so that I can then take slices of brainmask.mgz and the superi > mposed WM surface accross subjects and compare them, confident that they are > well alligned. > WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz ima > ges to a T1_1mm_template. I looked for the respective "surface" template to > register the surfaces, and maybe use mri_surf2surf, cannot find a "surface" > template that corresponds to the "T1" template. Ideally I would like to use > the same .lta transformation BOTH for the T1 image and the surface. As I und > erstand (?) they have a different mesh-transformation matrix. > Best regards, > Paolo > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Bruce Fischl -
Douglas Greve -
Paolo