Dear Freesurfer experts,
My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates.
I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates.
I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume?
Thank you very much!
Best Li Guo & Florence Campana
Thanks a lot!
Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to do the inverse of case #1.
On 7/19/17 12:28 PM, Li Guo wrote:
/Dear Freesurfer experts,/ / / /My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates./ / / /I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates. / / / /I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume? / / / /Thank you very much!/ / / /Best/ /Li Guo & Florence Campana/
Thanks a lot!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much for this information!!
Best, Li
On Jul 24, 2017, at 4:06 PM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to do the inverse of case #1.
On 7/19/17 12:28 PM, Li Guo wrote: Dear Freesurfer experts,
My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates.
I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates.
I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume?
Thank you very much!
Best Li Guo & Florence Campana
Thanks a lot!
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