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Hi Freesurfer experts,
After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much!
Best, Qi
The principal eigenvector of the tensor, which is the primary direction of diffusion, is V1. The magnitude of that vector is L1, i.e., AD.
The normal vector of a surface is a vector perpendicular to the tangent plane to the surface at a certain point. It's a characteristic of a surface, rather than a characteristic of diffusion, so you won't find it among the outputs of the diffusion tensor fit. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Friday, August 19, 2022 1:55 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] primary diffusion direction & surface normal vector
External Email - Use Caution
Hi Freesurfer experts,
After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much!
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
External Email - Use Caution
Hi Anastasia,
Thanks for your prompt reply. So can the normal vector of a surface be found in the outputs of recon-all?
Best, Qi
On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
The principal eigenvector of the tensor, which is the primary direction of diffusion, is V1. The magnitude of that vector is L1, i.e., AD.
The normal vector of a surface is a vector perpendicular to the tangent plane to the surface at a certain point. It's a characteristic of a surface, rather than a characteristic of diffusion, so you won't find it among the outputs of the diffusion tensor fit.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Friday, August 19, 2022 1:55 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] primary diffusion direction & surface normal vector
External Email - Use CautionHi Freesurfer experts,
After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much!
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-YkhjLp9Pj2wYgcEICb13J7PHRIFETS3DDyfQkfQBztAaI... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUb... < https://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUb... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Saturday, August 20, 2022 8:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] primary diffusion direction & surface normal vector
External Email - Use Caution
Hi Anastasia,
Thanks for your prompt reply. So can the normal vector of a surface be found in the outputs of recon-all?
Best, Qi
On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: The principal eigenvector of the tensor, which is the primary direction of diffusion, is V1. The magnitude of that vector is L1, i.e., AD.
The normal vector of a surface is a vector perpendicular to the tangent plane to the surface at a certain point. It's a characteristic of a surface, rather than a characteristic of diffusion, so you won't find it among the outputs of the diffusion tensor fit. ________________________________ 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 Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Sent: Friday, August 19, 2022 1:55 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] primary diffusion direction & surface normal vector
External Email - Use Caution
Hi Freesurfer experts,
After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much!
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1-YkhjLp9Pj2wYgcEICb13J7PHRIFETS3DDyfQkfQBztAaI-nZuDNa2hBA3MaQez5GconlG81l2Tg20MFYtctS_wyz1rmqiQCbdzO-i2m2bF7N7zzz85_AoK0_BetzjjxWAMEmECvxzunSxoDxehYGodPl_euyUIGWef26cTNVrAx8i_DBbIfhYg6MSlChEPNq97Tm5f8fvNU5fbu2YiNVhiN_UBVGM2WFmMDVDVC3S_zUObVbqypyqNswv9_iJ2SI-dNGJptEdRsp-RDuR7y-rLdGTeGd-ooiXorUPJTzWV8oFw6X68gVaJ9lQW0AqSF/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUbfmrnB4vD5y2EykYpzqNYUH0OW2oQ5_lABcDTu_dShvNADQmsaS3Dowo4RYKP1vj8EaKxUm7OJBMEwQcLo1v3bpnSQYzEjlmX-trWJVqaFg-rO-PrtEhELH4YNwXKjIdCd9EETHeLYyN9f0Xqh1aEKVels8YfFshEKYrkY66Co_QRRpRwevSEeUfWOkonnuMFH5XrwwaW9SD-z40H0YLMwEJlHqB_HXDuaKHpIAq39QYorOu74AxZBuQ7SGLF1fdkKvvQb7WaQycVz8mA-i/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUbfmrnB4vD5y2EykYpzqNYUH0OW2oQ5_lABcDTu_dShvNADQmsaS3Dowo4RYKP1vj8EaKxUm7OJBMEwQcLo1v3bpnSQYzEjlmX-trWJVqaFg-rO-PrtEhELH4YNwXKjIdCd9EETHeLYyN9f0Xqh1aEKVels8YfFshEKYrkY66Co_QRRpRwevSEeUfWOkonnuMFH5XrwwaW9SD-z40H0YLMwEJlHqB_HXDuaKHpIAq39QYorOu74AxZBuQ7SGLF1fdkKvvQb7WaQycVz8mA-i/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
you can also Convert a surface file to ascii (vertices are surface normals): mris_convert -n lh.white lh.white.normals.asc
On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu *Sent:* Saturday, August 20, 2022 8:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] primary diffusion direction & surface normal vector
External Email - Use Caution
Hi Anastasia,
Thanks for your prompt reply. So can the normal vector of a surface be found in the outputs of recon-all?
Best, Qi
On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
The principal eigenvector of the tensor, which is the primary direction of diffusion, is V1. The magnitude of that vector is L1, i.e., AD. The normal vector of a surface is a vector perpendicular to the tangent plane to the surface at a certain point. It's a characteristic of a surface, rather than a characteristic of diffusion, so you won't find it among the outputs of the diffusion tensor fit. ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edu> *Sent:* Friday, August 19, 2022 1:55 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] primary diffusion direction & surface normal vector External Email - Use Caution Hi Freesurfer experts, After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1-YkhjLp9Pj2wYgcEICb13J7PHRIFETS3DDyfQkfQBztAaI-nZuDNa2hBA3MaQez5GconlG81l2Tg20MFYtctS_wyz1rmqiQCbdzO-i2m2bF7N7zzz85_AoK0_BetzjjxWAMEmECvxzunSxoDxehYGodPl_euyUIGWef26cTNVrAx8i_DBbIfhYg6MSlChEPNq97Tm5f8fvNU5fbu2YiNVhiN_UBVGM2WFmMDVDVC3S_zUObVbqypyqNswv9_iJ2SI-dNGJptEdRsp-RDuR7y-rLdGTeGd-ooiXorUPJTzWV8oFw6X68gVaJ9lQW0AqSF/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUbfmrnB4vD5y2EykYpzqNYUH0OW2oQ5_lABcDTu_dShvNADQmsaS3Dowo4RYKP1vj8EaKxUm7OJBMEwQcLo1v3bpnSQYzEjlmX-trWJVqaFg-rO-PrtEhELH4YNwXKjIdCd9EETHeLYyN9f0Xqh1aEKVels8YfFshEKYrkY66Co_QRRpRwevSEeUfWOkonnuMFH5XrwwaW9SD-z40H0YLMwEJlHqB_HXDuaKHpIAq39QYorOu74AxZBuQ7SGLF1fdkKvvQb7WaQycVz8mA-i/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1qFcG-oNZ-lv1q-4_SPPWNqU5CWcf2dH8x2NZ6zbPQJ0jUbfmrnB4vD5y2EykYpzqNYUH0OW2oQ5_lABcDTu_dShvNADQmsaS3Dowo4RYKP1vj8EaKxUm7OJBMEwQcLo1v3bpnSQYzEjlmX-trWJVqaFg-rO-PrtEhELH4YNwXKjIdCd9EETHeLYyN9f0Xqh1aEKVels8YfFshEKYrkY66Co_QRRpRwevSEeUfWOkonnuMFH5XrwwaW9SD-z40H0YLMwEJlHqB_HXDuaKHpIAq39QYorOu74AxZBuQ7SGLF1fdkKvvQb7WaQycVz8mA-i/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
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Zeng, Qi