Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial in fsaverage space. I manage to transform lh.pial in fsaverage space but this does not give corresponding points or a way to do point by point transformation.
I want to do the same with some vertices from lh.pial-outer-smoother. Trying to transform this with mri_surf2surf gives an error because obviously there is no registration of that mesh. Any idea if this can be achieved at all?
Last question: am I correct assuming that the surface to surface registration (sphere.reg) does a better job at matching gyri and sulci on fsaverage than the simple conversion in MNI305 (aka fsaverage): MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
Thank you. Dorian
Hi Dorian
the transform should be by looking up the spherical coordinates on the sphere.reg for that vertex index and using that to find the corresponding fsaverage sphere.reg vertex.
cheers Bruce On Wed, 25 Jan 2017, Dorian P. wrote:
Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial in fsaverage space. I manage to transform lh.pial in fsaverage space but this does not give corresponding points or a way to do point by point transformation. I want to do the same with some vertices from lh.pial-outer-smoother. Trying to transform this with mri_surf2surf gives an error because obviously there is no registration of that mesh. Any idea if this can be achieved at all?
Last question: am I correct assuming that the surface to surface registration (sphere.reg) does a better job at matching gyri and sulci on fsaverage than the simple conversion in MNI305 (aka fsaverage): MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
Thank you. Dorian
Thank you Bruce.
I am not that familiar with this process. How can I look the transformation of a specific vertex index? Is this done still with mri_surf2surf?
Dorian
On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorian
the transform should be by looking up the spherical coordinates on the sphere.reg for that vertex index and using that to find the corresponding fsaverage sphere.reg vertex.
cheers Bruce On Wed, 25 Jan 2017, Dorian P. wrote:
Hi, I am trying to find the corresponding coordinate of a vertex in
lh.pial
in fsaverage space. I manage to transform lh.pial in fsaverage space but this does not give corresponding points or a way to do point by point transformation. I want to do the same with some vertices from lh.pial-outer-smoother.
Trying
to transform this with mri_surf2surf gives an error because obviously
there
is no registration of that mesh. Any idea if this can be achieved at all?
Last question: am I correct assuming that the surface to surface registration (sphere.reg) does a better job at matching gyri and sulci on fsaverage than the simple conversion in MNI305 (aka fsaverage): MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
Thank you. Dorian
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yes, mri_surf2surf will do it. In some sense there is really only one surface for each subject/hemisphere, it just lives at different points in space (which, pial, inflated, sphere.reg....). You can always use the index of a vertex to go from one to the other. If you give us more details about what you are trying to do, we can help, but if you have a scalar field on one of the surfaces (pial or whatever), you can use mri_surf2surf using the sphere.reg to map that to any other subject (including fsaverage which is in MNI coords)
cheers Bruce
On Wed, 25 Jan 2017, Dorian P. wrote:
Thank you Bruce. I am not that familiar with this process. How can I look the transformation of a specific vertex index? Is this done still with mri_surf2surf?
Dorian
On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dorian
the transform should be by looking up the spherical coordinates on the sphere.reg for that vertex index and using that to find the corresponding fsaverage sphere.reg vertex. cheers Bruce On Wed, 25 Jan 2017, Dorian P. wrote: > Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial > in fsaverage space. I manage to transform lh.pial in fsaverage space but > this does not give corresponding points or a way to do point by point > transformation. > I want to do the same with some vertices from lh.pial-outer-smoother. Trying > to transform this with mri_surf2surf gives an error because obviously there > is no registration of that mesh. Any idea if this can be achieved at all? > > Last question: am I correct assuming that the surface to surface > registration (sphere.reg) does a better job at matching gyri and sulci on > fsaverage than the simple conversion in MNI305 (aka fsaverage): > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > Thank you. > Dorian > >
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You can't easily transform a single vertex. One way to do it is to create an overlay with your vertex = 1 and all others = 0, then convert that to fsaverage and see where it lands. The mapping itself is a little tricky and can result in some unexpected behavior. The first step is to go through each target vertex and map the vertex from the source that is the closest. If your vertex is the closest vertex to multiple target vertices, then you will have several 1s in the output. There is also the chance that your vertex was not the closest to any target vertex. To handle this situation, there is a second loop that goes through all the source vertices that were never selected in the first loop and finds the closest target vertex. This means that there could be two or more source vertices that map to a given target vertex. In this case, the target vertex is given the value of the average of all the source vertices. So, when you look at the output map, there could be a single target vertex with a value of 1.0 or multiple target vertices with a value of 1.0, or a single target with a value that is less than 1.0.
On 01/25/2017 06:26 PM, Dorian P. wrote:
Thank you Bruce.
I am not that familiar with this process. How can I look the transformation of a specific vertex index? Is this done still with mri_surf2surf?
Dorian
On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Dorian the transform should be by looking up the spherical coordinates on the sphere.reg for that vertex index and using that to find the corresponding fsaverage sphere.reg vertex. cheers Bruce On Wed, 25 Jan 2017, Dorian P. wrote: > Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial > in fsaverage space. I manage to transform lh.pial in fsaverage space but > this does not give corresponding points or a way to do point by point > transformation. > I want to do the same with some vertices from lh.pial-outer-smoother. Trying > to transform this with mri_surf2surf gives an error because obviously there > is no registration of that mesh. Any idea if this can be achieved at all? > > Last question: am I correct assuming that the surface to surface > registration (sphere.reg) does a better job at matching gyri and sulci on > fsaverage than the simple conversion in MNI305 (aka fsaverage): > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > Thank you. > Dorian > > _______________________________________________ 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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ps. you can easily create an overlay with
mri_volsynth --template lh.thickness --pdf delta --delta-crsf yourvertexno 0 0 0 --o delta.mgh
On 01/25/2017 06:34 PM, Douglas N Greve wrote:
You can't easily transform a single vertex. One way to do it is to create an overlay with your vertex = 1 and all others = 0, then convert that to fsaverage and see where it lands. The mapping itself is a little tricky and can result in some unexpected behavior. The first step is to go through each target vertex and map the vertex from the source that is the closest. If your vertex is the closest vertex to multiple target vertices, then you will have several 1s in the output. There is also the chance that your vertex was not the closest to any target vertex. To handle this situation, there is a second loop that goes through all the source vertices that were never selected in the first loop and finds the closest target vertex. This means that there could be two or more source vertices that map to a given target vertex. In this case, the target vertex is given the value of the average of all the source vertices. So, when you look at the output map, there could be a single target vertex with a value of 1.0 or multiple target vertices with a value of 1.0, or a single target with a value that is less than 1.0.
On 01/25/2017 06:26 PM, Dorian P. wrote:
Thank you Bruce.
I am not that familiar with this process. How can I look the transformation of a specific vertex index? Is this done still with mri_surf2surf?
Dorian
On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Dorian the transform should be by looking up the spherical coordinates on the sphere.reg for that vertex index and using that to find the corresponding fsaverage sphere.reg vertex. cheers Bruce On Wed, 25 Jan 2017, Dorian P. wrote: > Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial > in fsaverage space. I manage to transform lh.pial in fsaverage space but > this does not give corresponding points or a way to do point by point > transformation. > I want to do the same with some vertices from lh.pial-outer-smoother. Trying > to transform this with mri_surf2surf gives an error because obviously there > is no registration of that mesh. Any idea if this can be achieved at all? > > Last question: am I correct assuming that the surface to surface > registration (sphere.reg) does a better job at matching gyri and sulci on > fsaverage than the simple conversion in MNI305 (aka fsaverage): > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > Thank you. > Dorian > > _______________________________________________ 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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