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Hi,
I've more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don't really understand how one can "color" a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in 'Faces'. Could someone help me understand what exactly is going on here? As one can imagine it's bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
Hi Daniel
Can you clarify what you mean? The surfaces don't have any values/vertex (e.g. scalar fields over the surface like thickness). Those are typically stored in separate files. What are you trying to display on the surface vertices? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 1:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution Hi,
I've more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don't really understand how one can "color" a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in 'Faces'. Could someone help me understand what exactly is going on here? As one can imagine it's bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
External Email - Use Caution
I'm trying to display, for example, an aparc.2009 on the pial surface. Because of reasons, I'd really like to display it in MATLAB. Thankfully, mris_convert to an ascii file works great for the surface (and AFNI's "@SUMA_Make_Spec_FS" actually helps convert the whole Freesurfer shebang into NIFTI/GIFTI, etc) to see vertex coordinates, vertex indices for faces, etc. What I really need is an ASCII file that has 1) vertex coords (from pial, or etc.) 2) vertex indices the make up each triangle, and 3) aparc labels for each of the triangles in 2).
But... it seems that the index numbers in the left column of an output .label file generated by mri_annotation2label are indices of vertices, not faces, and I honestly just don't understand how Freesurfer goes about coloring a face of a triangle if, say, one of the vertices of that triangle is shared by two different aparc parcels. (Or alternatively, if all three vertices of a triangle "belong" to different labels).
I'm sorry if I'm mangling this question.
Daniel Schwartz
Advanced Imaging Research Center
Layton Aging and Alzheimer's Disease Center
OHSU
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Tuesday, November 1, 2022 11:49:23 AM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
Hi Daniel
Can you clarify what you mean? The surfaces don’t have any values/vertex (e.g. scalar fields over the surface like thickness). Those are typically stored in separate files. What are you trying to display on the surface vertices? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 1:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution Hi,
I’ve more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don’t really understand how one can “color” a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in ‘Faces’. Could someone help me understand what exactly is going on here? As one can imagine it’s bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
I see. I defer to Ruopeng about the specifics of coloring faces. We don't usually include labels in the same file, as you note below. We include the index to look up the geometry in another file (white, pial, inflated, whatever you want)
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution
I'm trying to display, for example, an aparc.2009 on the pial surface. Because of reasons, I'd really like to display it in MATLAB. Thankfully, mris_convert to an ascii file works great for the surface (and AFNI's "@SUMA_Make_Spec_FS" actually helps convert the whole Freesurfer shebang into NIFTI/GIFTI, etc) to see vertex coordinates, vertex indices for faces, etc. What I really need is an ASCII file that has 1) vertex coords (from pial, or etc.) 2) vertex indices the make up each triangle, and 3) aparc labels for each of the triangles in 2).
But... it seems that the index numbers in the left column of an output .label file generated by mri_annotation2label are indices of vertices, not faces, and I honestly just don't understand how Freesurfer goes about coloring a face of a triangle if, say, one of the vertices of that triangle is shared by two different aparc parcels. (Or alternatively, if all three vertices of a triangle "belong" to different labels).
I'm sorry if I'm mangling this question.
Daniel Schwartz
Advanced Imaging Research Center
Layton Aging and Alzheimer's Disease Center
OHSU
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Tuesday, November 1, 2022 11:49:23 AM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
Hi Daniel
Can you clarify what you mean? The surfaces don't have any values/vertex (e.g. scalar fields over the surface like thickness). Those are typically stored in separate files. What are you trying to display on the surface vertices? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 1:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution Hi,
I've more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don't really understand how one can "color" a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in 'Faces'. Could someone help me understand what exactly is going on here? As one can imagine it's bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
I’m not sure I get exactly what you wanted to do. But in freeview, surface colors are assigned by vertices, not faces. If the vertices of a face have different colors, the colors will be interpolated across the face by the rendering engine. If you turn on mesh display you will see that.
On Nov 1, 2022, at 3:04 PM, Daniel Schwartz <schwartd@ohsu.edumailto:schwartd@ohsu.edu> wrote:
External Email - Use Caution
I'm trying to display, for example, an aparc.2009 on the pial surface. Because of reasons, I'd really like to display it in MATLAB. Thankfully, mris_convert to an ascii file works great for the surface (and AFNI's "@SUMA_Make_Spec_FS" actually helps convert the whole Freesurfer shebang into NIFTI/GIFTI, etc) to see vertex coordinates, vertex indices for faces, etc. What I really need is an ASCII file that has 1) vertex coords (from pial, or etc.) 2) vertex indices the make up each triangle, and 3) aparc labels for each of the triangles in 2).
But... it seems that the index numbers in the left column of an output .label file generated by mri_annotation2label are indices of vertices, not faces, and I honestly just don't understand how Freesurfer goes about coloring a face of a triangle if, say, one of the vertices of that triangle is shared by two different aparc parcels. (Or alternatively, if all three vertices of a triangle "belong" to different labels).
I'm sorry if I'm mangling this question.
Daniel Schwartz Advanced Imaging Research Center Layton Aging and Alzheimer's Disease Center OHSU
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Tuesday, November 1, 2022 11:49:23 AM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
Hi Daniel
Can you clarify what you mean? The surfaces don’t have any values/vertex (e.g. scalar fields over the surface like thickness). Those are typically stored in separate files. What are you trying to display on the surface vertices? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 1:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution Hi,
I’ve more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don’t really understand how one can “color” a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in ‘Faces’. Could someone help me understand what exactly is going on here? As one can imagine it’s bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ah, I definitely get it now. Thanks so much to you both!
Daniel Schwartz
Advanced Imaging Research Center
Layton Aging and Alzheimer's Disease Center
OHSU
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@mgh.harvard.edu Sent: Tuesday, November 1, 2022 1:26:43 PM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
I’m not sure I get exactly what you wanted to do. But in freeview, surface colors are assigned by vertices, not faces. If the vertices of a face have different colors, the colors will be interpolated across the face by the rendering engine. If you turn on mesh display you will see that.
On Nov 1, 2022, at 3:04 PM, Daniel Schwartz <schwartd@ohsu.edumailto:schwartd@ohsu.edu> wrote:
External Email - Use Caution
I'm trying to display, for example, an aparc.2009 on the pial surface. Because of reasons, I'd really like to display it in MATLAB. Thankfully, mris_convert to an ascii file works great for the surface (and AFNI's "@SUMA_Make_Spec_FS" actually helps convert the whole Freesurfer shebang into NIFTI/GIFTI, etc) to see vertex coordinates, vertex indices for faces, etc. What I really need is an ASCII file that has 1) vertex coords (from pial, or etc.) 2) vertex indices the make up each triangle, and 3) aparc labels for each of the triangles in 2).
But... it seems that the index numbers in the left column of an output .label file generated by mri_annotation2label are indices of vertices, not faces, and I honestly just don't understand how Freesurfer goes about coloring a face of a triangle if, say, one of the vertices of that triangle is shared by two different aparc parcels. (Or alternatively, if all three vertices of a triangle "belong" to different labels).
I'm sorry if I'm mangling this question.
Daniel Schwartz Advanced Imaging Research Center Layton Aging and Alzheimer's Disease Center OHSU
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Tuesday, November 1, 2022 11:49:23 AM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
Hi Daniel
Can you clarify what you mean? The surfaces don’t have any values/vertex (e.g. scalar fields over the surface like thickness). Those are typically stored in separate files. What are you trying to display on the surface vertices? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Daniel Schwartz Sent: Tuesday, November 1, 2022 1:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution Hi,
I’ve more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don’t really understand how one can “color” a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in ‘Faces’. Could someone help me understand what exactly is going on here? As one can imagine it’s bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv.
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/13FAbadreHy3sVLPkPY1WnjBw0HL-cx03j_znUSZTChOqvA...https://secure-web.cisco.com/1eV8Wo7hDT5ph-yJCyxhyrV3g9dWU7PfA1akH5qyqL2huXhEzddNkpLtfCMcwBR0YJG90kh8q9JrJKh9RQOgI6Um1ZHwUgEUYkgzkmGhv8sQeVp0TD7JPfXm4AccorUeEm8sZIWdm5mjmnhaBbzVEuy4LHsqT5rToUiO1TMlEGFpHxM41s9luoxGEJBocoNFGtAOse0llmnUUwd4Q5T48uIuIWYM_9d7lCE05X7BjDlUGeqTyp00_Tm-BQtjAmDdPSNtmkgEYaIBRFzHkKYzS83OeWOnnq9gISdHwocfRQR8OWMxrBEqQ9TZkwN6XKTjl/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!Mi0JBg!OygGooRfcH6Q76deMCU3GGTZTlfVRx-yPwzO0-Ca7EzBj0V_KzteKX0h0KuO7fhTU3yEk0SdOV6TKEsN1YHeJaY$
freesurfer@nmr.mgh.harvard.edu
-
Daniel Schwartz -
Fischl, Bruce R.,PHD -
Wang, Ruopeng