Dear freesurfer experts,
I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct:
I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces. At that moment my different subjects surfaces had different number of vertices and I would like to average them together.
Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data. Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface. I then created a new paint surface where only those vertices were taken into account.
Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas?
Is there a better way to do this?
Thanks in advance,
Jose Marques
Hi Jose, why don't you use mri_surf2surf to transfer your T1-w overlays to fsaverage? Alternatively, you can just specify fsaverage as the output subject for mri_vol2surf. Then all of your T1-w overlays will be in alignment. doug
On 7/26/12 4:31 AM, Rebelo Ferreira Marques Jose Pedro wrote:
Dear freesurfer experts,
I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct:
I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces.
At that moment my different subjects surfaces had different number of vertices and I would like to average them together.
Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data.
Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface.
I then created a new paint surface where only those vertices were taken into account.
Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas?
Is there a better way to do this?
Thanks in advance,
Jose Marques
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jose
you should use the sphere.reg, not the sphere, but other than that what you describe is essentially what mri_surf2surf does. You also have to be a bit careful to sample in both directions to avoid holes in the mapping.
cheers Bruce
On Thu, 26 Jul 2012, Rebelo Ferreira Marques Jose Pedro wrote:
Dear freesurfer experts,
I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct:
I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces.
At that moment my different subjects surfaces had different number of vertices and I would like to average them together.
Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data.
Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface.
I then created a new paint surface where only those vertices were taken into account.
Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas?
Is there a better way to do this?
Thanks in advance,
Jose Marques
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Rebelo Ferreira Marques Jose Pedro