External Email - Use Caution
Dear Freesurfer Developers,
How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to.
For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only?
Thank you very much for your help in advance!
The "RAS" in that image refers to scanner RAS (not MNI coords). The "Talarairach" is actually MNI305 (it is called this in version 7 to avoid this kind of confusion).
In case you have not seen it, here is a page that may answer more of your questions.
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 5/4/2020 3:48 PM, Hye Bin Yoo wrote:
External Email - Use Caution
Dear Freesurfer Developers,
How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to.
For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only?
Thank you very much for your help in advance!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Dr. Greve,
Thanks for your prompt response. That's good to know, and indeed I have seen this page. The confusion came because the MNI coordinate I know have an origin at anterior commisure, so the x value should range from neg 90 something, whereas Talairach coordinate x I have seen in Freeview was always positive. What is the exact difference between Talairach (MNI305) coordinates from FreeSurfer and MNI coordinates we see in FSL/SPM/MRIcron?
Sincerely,
2020년 5월 4일 (월) 오후 3:07, Douglas N. Greve dgreve@mgh.harvard.edu님이 작성:
The "RAS" in that image refers to scanner RAS (not MNI coords). The "Talarairach" is actually MNI305 (it is called this in version 7 to avoid this kind of confusion).
In case you have not seen it, here is a page that may answer more of your questions.
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 5/4/2020 3:48 PM, Hye Bin Yoo wrote:
External Email - Use CautionDear Freesurfer Developers,
How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to.
For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only?
Thank you very much for your help in advance!
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This was a bug in FreeView. If you download version 7, you should see reasonable numbers
On 5/4/2020 4:51 PM, Hye Bin Yoo wrote:
External Email - Use Caution
Dear Dr. Greve,
Thanks for your prompt response. That's good to know, and indeed I have seen this page. The confusion came because the MNI coordinate I know have an origin at anterior commisure, so the x value should range from neg 90 something, whereas Talairach coordinate x I have seen in Freeview was always positive. What is the exact difference between Talairach (MNI305) coordinates from FreeSurfer and MNI coordinates we see in FSL/SPM/MRIcron?
Sincerely,
2020년 5월 4일 (월) 오후 3:07, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>님이 작성:
The "RAS" in that image refers to scanner RAS (not MNI coords). The "Talarairach" is actually MNI305 (it is called this in version 7 to avoid this kind of confusion). In case you have not seen it, here is a page that may answer more of your questions. https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 5/4/2020 3:48 PM, Hye Bin Yoo wrote:External Email - Use Caution Dear Freesurfer Developers, How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to. For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only? Thank you very much for your help in advance! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hye Bin Yoo