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If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates. Following the steps laid out on the CoordinateSystems web page I can convert back and forth between those coordinate systems. However, I can't figure out what I need to do to calculate the Vertex coordinates. I can load lh.pial in matlab and see the (+1) vertex number and coordinates, but I'd like to figure out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS. Is there an easy formula to calculate this? Thanks in advance for any and all responses.
-Joel
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Hi Joel,
you need to find the corresponding voxel ( using ras2vox transformation matrix) and then apply your vox2ras-tkr matrix to it. it would give you the tkrRAS coordinate.
cheers, Ehsan.
On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E joel-bruss@uiowa.edu wrote:
External Email - Use CautionIf I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates. Following the steps laid out on the CoordinateSystems web page I can convert back and forth between those coordinate systems. However, I can't figure out what I need to do to calculate the Vertex coordinates. I can load lh.pial in matlab and see the (+1) vertex number and coordinates, but I'd like to figure out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS. Is there an easy formula to calculate this? Thanks in advance for any and all responses.
-Joel
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
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Close, but still not what I'm looking for. I start with orig.mgz file and have RAS. I can convert that to voxel coordinates. I can then convert that to TkReg RAS/SurfaceRAS coordinates, but what I'm looking for is the Vertex coordinate. For example, looking at FreeView, I see the following four coordinates (on Rhemi, for example):
RAS: 54, -78, 1
TkReg RAS (orig): 55, -61, -18
orig: 50 [73, 146, 67]
rh.pial: SurfaceRAS [55, -61, -18]
rh.pial: Vertex 11660 [53.91, -60.35, -18.31]
I can convert back and forth between the top three with ease. I can't figure out how to get the last coordinate (Vertex).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ehsan Tadayon ehsan.tadayon84@gmail.com Sent: Tuesday, September 4, 2018 12:00:53 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] SurfaceRAS to Vertex coordinate system
External Email - Use Caution
Hi Joel,
you need to find the corresponding voxel ( using ras2vox transformation matrix) and then apply your vox2ras-tkr matrix to it. it would give you the tkrRAS coordinate.
cheers, Ehsan.
On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E <joel-bruss@uiowa.edumailto:joel-bruss@uiowa.edu> wrote:
External Email - Use Caution
If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates. Following the steps laid out on the CoordinateSystems web page I can convert back and forth between those coordinate systems. However, I can't figure out what I need to do to calculate the Vertex coordinates. I can load lh.pial in matlab and see the (+1) vertex number and coordinates, but I'd like to figure out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS. Is there an easy formula to calculate this? Thanks in advance for any and all responses.
-Joel
________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________ _______________________________________________ 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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________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________
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There is no linear transformation between the two. Vertex coordinate is equal to surfaceRAS when the point that you have selected is actually one of the vertices on the chosen surface. However, if the point is not on the surface, it finds the nearest vertex. So, you can read your surface ( in matlab : [vertices, faces] = read_surf('lh.pial') ) and then find the vertex that is closest to your selected point (surfaceRAS). This is the vertex that you see in the Freeview.
Ehsan.
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Ah, that makes sense. Short of calculating a Euclidean distance between every surface RAS and my point I'd like on the surface, then grabbing the one with the shortest distance, is there a function/utility in FreeSurfer that will generate the closest vertex for me?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ehsan Tadayon ehsan.tadayon84@gmail.com Sent: Tuesday, September 4, 2018 2:05:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system
External Email - Use Caution
There is no linear transformation between the two. Vertex coordinate is equal to surfaceRAS when the point that you have selected is actually one of the vertices on the chosen surface. However, if the point is not on the surface, it finds the nearest vertex. So, you can read your surface ( in matlab : [vertices, faces] = read_surf('lh.pial') ) and then find the vertex that is closest to your selected point (surfaceRAS). This is the vertex that you see in the Freeview.
Ehsan.
________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________
Hi Joel
there is internal code for this where we create a spatial lookup/hash table and use it to find the closest vertex, but it is just a set of c functions.
cheers Bruce
On Tue, 4 Sep 2018, Bruss, Joel E wrote:
External Email - Use Caution
Ah, that makes sense. Short of calculating a Euclidean distance between every surface RAS and my point I'd like on the surface, then grabbing the one with the shortest distance, is there a function/utility in FreeSurfer that will generate the closest vertex for me?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ehsan Tadayon ehsan.tadayon84@gmail.com Sent: Tuesday, September 4, 2018 2:05:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system
External Email - Use Caution
[cbb23410d862335b08d6bf64e91c01427a4b6868.png?u=375924] There is no linear transformation between the two. Vertex coordinate is equal to surfaceRAS when the point that you have selected is actually one of the vertices on the chosen surface. However, if the point is not on the surface, it finds the nearest vertex. So, you can read your surface ( in matlab : [vertices, faces] = read_surf('lh.pial') ) and then find the vertex that is closest to your selected point (surfaceRAS). This is the vertex that you see in the Freeview.
Ehsan.
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Bruss, Joel E -
Ehsan Tadayon