Hi everyone,
In an earlier post, I had asked how to transform the white surface of one subject to the white surface of another subject, and Bruce Fischl suggested mri_surf2surf should be able to do this. After looking over the website material related to mri_surf2surf, I find I'm not sure how mri_surf2surf works, and so am still not sure how to proceed.
As a starting point, suppose we have the file lh.sphere.reg for each of two subjects, A and B, and consider, say, vertex 1 of subject A. Here is what I understand: This vertex maps to a point P on the sphere that has coordinates given in subjects A's lh.sphere.reg file. The point P is contained in some closed triangle T from B's mesh, as that mesh appears in B's lh.sphere.reg file. This triangle is formed from three points on the sphere that correspond to three vertices that appear in B's lh.white file. These three vertices thus form a triangle T' in B's native volume space, and thus the point P contained in T corresponds to a point P' in B's native volume space that is contained in T'.
So here is my question: How would I used mri_surf2surf to find the coordinates (in B's native volume space) of the point P'?
Thanks in advance for you help in clarifying this for me.
Best regards, David Romano
Hi David, did you check the help within mri_surf2surf? Run mri_surf2surf --help. I think it has an example of what you want to do. doug
On 08/30/2013 06:57 PM, David Romano wrote:
Hi everyone,
In an earlier post, I had asked how to transform the white surface of one subject to the white surface of another subject, and Bruce Fischl suggested mri_surf2surf should be able to do this. After looking over the website material related to mri_surf2surf, I find I'm not sure how mri_surf2surf works, and so am still not sure how to proceed.
As a starting point, suppose we have the file lh.sphere.reg for each of two subjects, A and B, and consider, say, vertex 1 of subject A. Here is what I understand: This vertex maps to a point P on the sphere that has coordinates given in subjects A's lh.sphere.reg file. The point P is contained in some closed triangle T from B's mesh, as that mesh appears in B's lh.sphere.reg file. This triangle is formed from three points on the sphere that correspond to three vertices that appear in B's lh.white file. These three vertices thus form a triangle T' in B's native volume space, and thus the point P contained in T corresponds to a point P' in B's native volume space that is contained in T'.
So here is my question: How would I used mri_surf2surf to find the coordinates (in B's native volume space) of the point P'?
Thanks in advance for you help in clarifying this for me.
Best regards, David Romano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug; I'd only gone through the information I could find online and didn't see there was a --help flag available. I'll try that now. And out of curiosity in case something similar happens with other freesurfer commands, is the --help flag standard in freesurfer?
Thanks again, David
On Tue, Sep 3, 2013 at 7:32 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi David, did you check the help within mri_surf2surf? Run mri_surf2surf --help. I think it has an example of what you want to do. doug
On 08/30/2013 06:57 PM, David Romano wrote:
Hi everyone,
In an earlier post, I had asked how to transform the white surface of one subject to the white surface of another subject, and Bruce Fischl suggested mri_surf2surf should be able to do this. After looking over the website material related to mri_surf2surf, I find I'm not sure how mri_surf2surf works, and so am still not sure how to proceed.
As a starting point, suppose we have the file lh.sphere.reg for each of two subjects, A and B, and consider, say, vertex 1 of subject A. Here is what I understand: This vertex maps to a point P on the sphere that has coordinates given in subjects A's lh.sphere.reg file. The point P is contained in some closed triangle T from B's mesh, as that mesh appears in B's lh.sphere.reg file. This triangle is formed from three points on the sphere that correspond to three vertices that appear in B's lh.white file. These three vertices thus form a triangle T' in B's native volume space, and thus the point P contained in T corresponds to a point P' in B's native volume space that is contained in T'.
So here is my question: How would I used mri_surf2surf to find the coordinates (in B's native volume space) of the point P'?
Thanks in advance for you help in clarifying this for me.
Best regards, David Romano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
It is fairly standard, at least in the programs I write. It sometimes appears with a single dash (-help) doug
On 09/03/2013 10:59 AM, David Romano wrote:
Thanks, Doug; I'd only gone through the information I could find online and didn't see there was a --help flag available. I'll try that now. And out of curiosity in case something similar happens with other freesurfer commands, is the --help flag standard in freesurfer?
Thanks again, David
On Tue, Sep 3, 2013 at 7:32 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi David, did you check the help within mri_surf2surf? Run mri_surf2surf --help. I think it has an example of what you want to do. doug On 08/30/2013 06:57 PM, David Romano wrote: > Hi everyone, > > In an earlier post, I had asked how to transform the white surface of > one subject to the white surface of another subject, and Bruce Fischl > suggested mri_surf2surf should be able to do this. After looking > over the website material related to mri_surf2surf, I find I'm not > sure how mri_surf2surf works, and so am still not sure how to proceed. > > As a starting point, suppose we have the file lh.sphere.reg for each > of two subjects, A and B, and consider, say, vertex 1 of subject A. > Here is what I understand: This vertex maps to a point P on the sphere > that has coordinates given in subjects A's lh.sphere.reg file. The > point P is contained in some closed triangle T from B's mesh, as that > mesh appears in B's lh.sphere.reg file. This triangle is formed from > three points on the sphere that correspond to three vertices that > appear in B's lh.white file. These three vertices thus form a > triangle T' in B's native volume space, and thus the point P contained > in T corresponds to a point P' in B's native volume space that is > contained in T'. > > So here is my question: How would I used mri_surf2surf to find the > coordinates (in B's native volume space) of the point P'? > > Thanks in advance for you help in clarifying this for me. > > Best regards, > David Romano > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 . 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@nmr.mgh.harvard.edu
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David Romano -
Douglas N Greve