Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
The srcval is the map that you want to convert (the p-values here). The trgval is the output. You should not be specifying any surfaces since mri_surf2surf will find the relevant surface registration files. doug
On 8/16/13 10:28 AM, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
why not just save the p-values in mgz format with MRIwrite.m or save_mgh.m as an nvertices x 1 x 1 "volume", then map it? I don't think mapping the inflated is what you want.
Bruce On Fri, 16 Aug 2013, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
Thanks! This could be a solution. I already tried to do a similar thing: to save the p-values as "curv" with write_curv.m and map that. Do I have to specify the output type as "paint" then? And what is the best way to visualize it?
sorry for the basic questions. I have not used freesurfer display tools before, so I am unsure about every step.
Thanks a lot! Irina
On 8/16/2013 5:15 PM, Bruce Fischl wrote:
why not just save the p-values in mgz format with MRIwrite.m or save_mgh.m as an nvertices x 1 x 1 "volume", then map it? I don't think mapping the inflated is what you want.
Bruce On Fri, 16 Aug 2013, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Hello,
I have fMRI data from a small group of subjects. I did a surface-based MVPA (in matlab) in subjects' individual space, and for each subject I have a vector of, say, p-values (one value for each vertex). I would like to display these results on a template surface. So I would like to know the mapping for each vertex to the template surface (as described in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
I used mris_register to register individual subjects' surfaces to .average.curvature.filled.buckner40.tif. What is the next step? Is there a way to have the mapping from the resulting registered spherical surface to an inflated (template) surface?
Or should I use mris_surf2surf? If I just want to get the mapping for each vertex of my subject to the template, what arguments to the function should I specify? Are there any additional steps required (like, for example, aligning the surface with the template)?
Thank you in advance, Irina
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.
You can use curv as the input type. The output you can just add a .mgh to the extension and surf2surf will figure it out. You can view it with tksurfer, something like
tksurfer fsaverage lh -aparc -ov youroverlay.mgh
On 08/16/2013 12:27 PM, Irina Simanova wrote:
Thanks! This could be a solution. I already tried to do a similar thing: to save the p-values as "curv" with write_curv.m and map that. Do I have to specify the output type as "paint" then? And what is the best way to visualize it?
sorry for the basic questions. I have not used freesurfer display tools before, so I am unsure about every step.
Thanks a lot! Irina
On 8/16/2013 5:15 PM, Bruce Fischl wrote:
why not just save the p-values in mgz format with MRIwrite.m or save_mgh.m as an nvertices x 1 x 1 "volume", then map it? I don't think mapping the inflated is what you want.
Bruce On Fri, 16 Aug 2013, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
> Hello, > > I have fMRI data from a small group of subjects. I did a > surface-based > MVPA (in matlab) in subjects' individual space, and for each > subject I > have a vector of, say, p-values (one value for each vertex). I would > like to display these results on a template surface. So I would > like to > know the mapping for each vertex to the template surface (as > described > in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) > > I used mris_register to register individual subjects' surfaces to > .average.curvature.filled.buckner40.tif. What is the next step? > Is there > a way to have the mapping from the resulting registered spherical > surface to an inflated (template) surface? > > Or should I use mris_surf2surf? If I just want to get the mapping > for > each vertex of my subject to the template, what arguments to the > function should I specify? Are there any additional steps required > (like, for example, aligning the surface with the template)? > > Thank you in advance, > Irina > > _______________________________________________ > 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.
btw, you should probably convert your p-values to -log10(p)
On 08/16/2013 12:27 PM, Irina Simanova wrote:
Thanks! This could be a solution. I already tried to do a similar thing: to save the p-values as "curv" with write_curv.m and map that. Do I have to specify the output type as "paint" then? And what is the best way to visualize it?
sorry for the basic questions. I have not used freesurfer display tools before, so I am unsure about every step.
Thanks a lot! Irina
On 8/16/2013 5:15 PM, Bruce Fischl wrote:
why not just save the p-values in mgz format with MRIwrite.m or save_mgh.m as an nvertices x 1 x 1 "volume", then map it? I don't think mapping the inflated is what you want.
Bruce On Fri, 16 Aug 2013, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
> Hello, > > I have fMRI data from a small group of subjects. I did a > surface-based > MVPA (in matlab) in subjects' individual space, and for each > subject I > have a vector of, say, p-values (one value for each vertex). I would > like to display these results on a template surface. So I would > like to > know the mapping for each vertex to the template surface (as > described > in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) > > I used mris_register to register individual subjects' surfaces to > .average.curvature.filled.buckner40.tif. What is the next step? > Is there > a way to have the mapping from the resulting registered spherical > surface to an inflated (template) surface? > > Or should I use mris_surf2surf? If I just want to get the mapping > for > each vertex of my subject to the template, what arguments to the > function should I specify? Are there any additional steps required > (like, for example, aligning the surface with the template)? > > Thank you in advance, > Irina > > _______________________________________________ > 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.
Hi Irina
no problem. We advocate the use of mgz not curv as it is being deprecated. You can then visualize it in either freeview or tksurfer. cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
Thanks! This could be a solution. I already tried to do a similar thing: to save the p-values as "curv" with write_curv.m and map that. Do I have to specify the output type as "paint" then? And what is the best way to visualize it?
sorry for the basic questions. I have not used freesurfer display tools before, so I am unsure about every step.
Thanks a lot! Irina
On 8/16/2013 5:15 PM, Bruce Fischl wrote:
why not just save the p-values in mgz format with MRIwrite.m or save_mgh.m as an nvertices x 1 x 1 "volume", then map it? I don't think mapping the inflated is what you want.
Bruce On Fri, 16 Aug 2013, Irina Simanova wrote:
I tried to set --srcsurfval to $SUBJECTS_DIR/Subject1/surf/lh.inflated to map the coordinates of vertices.
But this gives the error, guess I am doing something wrong.
At the end I want to map the p-values, and this is just a vector in Matlab (one vertex - one value).
Irina
On 8/16/2013 4:16 PM, Bruce Fischl wrote:
what are you trying to map? The p-values? What format are they stored in? On Fri, 16 Aug 2013, Irina Simanova wrote:
Thank you, Bruce,
I am trying surf2surf, but keep getting errors about file type ("could not determine type of..." )
What should be the --srcsurfval argument? Do I have to specify --src_type?
mri_surf2surf --srcsubject Subject1 --hemi lh --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/Subject1/surf/lh.surf_reg --srcsurfval ??
thanks a lot! Irina
On 8/16/2013 3:38 PM, Bruce Fischl wrote:
Hi Irina that is what surf2surf does. The mapping is encoded in the vertex locations in the ?h.sphere.reg files. surf2surf finds the nearest set of vertices on the target sphere for each one on the source sphere and interpolates onto it, then does the inverse mapping to fill holes
cheers Bruce
On Fri, 16 Aug 2013, Irina Simanova wrote:
> Hello, > > I have fMRI data from a small group of subjects. I did a surface-based > MVPA (in matlab) in subjects' individual space, and for each subject I > have a vector of, say, p-values (one value for each vertex). I would > like to display these results on a template surface. So I would like > to > know the mapping for each vertex to the template surface (as described > in http://ftp.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) > > I used mris_register to register individual subjects' surfaces to > .average.curvature.filled.buckner40.tif. What is the next step? Is > there > a way to have the mapping from the resulting registered spherical > surface to an inflated (template) surface? > > Or should I use mris_surf2surf? If I just want to get the mapping for > each vertex of my subject to the template, what arguments to the > function should I specify? Are there any additional steps required > (like, for example, aligning the surface with the template)? > > Thank you in advance, > Irina > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Irina Simanova