Hi Doug,
Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshold in tksurfer, the coordinates seem fairly different: non integers, and in different ranges e.g. [-36.806 -18.293 64.462], [-21.393 -61.263 8.910]) etc.
However, when I create a label file (via write_label.m) with -1 in the first column and with the TkRAS coordinates that I computed in the columns 2,3,4 , and then via tksurfer load this label and then save the selected label, I obtain a new label with R A S coordinates as [34.198 -48.599 29.835], [35.364 -45.689 31.179], i.e. similar to the one that I have in my ROI label files.
Could you please help me to figure out what my tkRAS values (e.g.[113, -119,88], [105, -103, 96) correspond to, versus the ones returned by tksurfer ([34.198 -48.599 29.835], [35.364 -45.689 31.179])?
I hope that it makes sense. Thank you so much!
Florence
*From:* Douglas Greve greve@nmr.mgh.harvard.edu *Date:* July 24, 2017 at 4:06:25 PM EDT *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* *Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates* *Reply-To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu
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*
Hard to say whether the coords are right or not. You can run tksurfer and look at the coords in and around your region to see whether they are reasonable. The -1s need to go into the label that is used as input the mri_label2label. mri_label2label will assign vertex numbers based on the coordinates. Those vertex numbers are needed in order to load it on the surface
On 07/26/2017 11:08 PM, Florence Campana wrote:
Hi Doug,
Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshold in tksurfer, the coordinates seem fairly different: non integers, and in different ranges e.g. [-36.806 -18.293 64.462], [-21.393 -61.263 8.910]) etc.
However, when I create a label file (via write_label.m) with -1 in the first column and with the TkRAS coordinates that I computed in the columns 2,3,4 , and then via tksurfer load this label and then save the selected label, I obtain a new label with R A S coordinates as [34.198 -48.599 29.835], [35.364 -45.689 31.179], i.e. similar to the one that I have in my ROI label files.
Could you please help me to figure out what my tkRAS values (e.g.[113, -119,88], [105, -103, 96) correspond to, versus the ones returned by tksurfer ([34.198 -48.599 29.835], [35.364 -45.689 31.179])?
I hope that it makes sense. Thank you so much!
Florence
*From:* Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> *Date:* July 24, 2017 at 4:06:25 PM EDT *To:* <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates* *Reply-To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
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/
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Florence Campana