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Dear experts,
I am assessing different morphological aspects of the cortex including sulcal depth but am struggling to understand how this is calculated in FreeSurfer. I see that a previous correspondence (https://secure-web.cisco.com/130Tf81zvPk_603DeJ5a0ZZo4MNfYCZ60im_ZWCS7hPT0Bo...) points to this being described on page 199 within the “Cortical surface-based analysis II” – paper, by Fischl et al. but to my understanding it only describes the inflation process. Is it so that as concave areas like sulci move outward, while convex areas like gyri move inward during this process, this movement is somehow quantified and used to calculate sulcal depth? I also see a previous article stating that “..Freesurfer's sulcal depth measurement measures how far a vertex moves during an inflation operation”, also referencing the same Fischl paper.
While other folding measures like LGI (https://secure-web.cisco.com/1rZbD04F-L_WBb_-7dP8B298OK6uZo1zDlLneMBGyND_ivL... and curvature (https://secure-web.cisco.com/1bY39JsrtiDKpPFJNg4aHhIchmGuug1PSRGvTczzLFMkNC8...) are neatly covered, I unfortunately could not find the same descriptions for sulcal depth. Any clarifications would be greatly appreciated.
Thank you in advance!
Kind regards Linn Norbom
Hi Linn
The text you cite is how we measure it. It is the signed distance each points moves to get from the white to the inflated surface, where outwards movement is positive (along the surface normal direction) and inwards distance is negative.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Linn Christin Bonaventure Norbom Sent: Tuesday, February 6, 2024 8:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] calculation of sulcal depth
External Email - Use Caution Dear experts,
I am assessing different morphological aspects of the cortex including sulcal depth but am struggling to understand how this is calculated in FreeSurfer. I see that a previous correspondence (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43772.html) points to this being described on page 199 within the "Cortical surface-based analysis II" - paper, by Fischl et al. but to my understanding it only describes the inflation process. Is it so that as concave areas like sulci move outward, while convex areas like gyri move inward during this process, this movement is somehow quantified and used to calculate sulcal depth? I also see a previous article stating that "..Freesurfer's sulcal depth measurement measures how far a vertex moves during an inflation operation", also referencing the same Fischl paper.
While other folding measures like LGI (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LGIhttps://secure-web.cisco.com/1rZbD04F-L_WBb_-7dP8B298OK6uZo1zDlLneMBGyND_ivL2gPkiZTug0WyglfVkOxxiC02F2Fh9blwiaSive2lw9mQNXXar3KvM6viLVnbE0k8g7scdmmyXJnbPb5wzV7dorN16_yT8hpRYKkSnOgVJPTiYFr6imCXCw0oqSa3vw69icYlZlp0nrJEZ8CQI6THyg7T7c18tXbLwhC255w6lGcKFdcqQrkDtTxdDJ2m2rKsF8kH0AyALHcPwzFqoW5lVOAgzmbhZXo18NET-ucEVyQLZkek29qz2zU84XKJGF_9yRPSlYxRMomM5dW00gbbDpAYbhEk1jwn-WXxTb6w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI and curvature (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/MeanCurvaturehttps://secure-web.cisco.com/1bY39JsrtiDKpPFJNg4aHhIchmGuug1PSRGvTczzLFMkNC8ifemRnYXnUDdmvRVVZ4BQmPxQvIJYXoUo14A2_GWqoJNuEnMk1x13Nj6Nu8dkE12w8VdN62Wvy5k2ihHSWjarOV9aYXxP7z56hbzOv-OIIfyD4jdXX65nYsgl0gy63HZMpxvtIe7E4aREI07xP6OJiWKOkIBQcg4rhaXvSYofqQl930k1EpdawV8TMZBGr7tPI8p4Q8x99pg9LtQAkPs9_1zpMUeiIRrajetzyPwuc597BofExcrVipWR3eBC0nVk_aC7UjmoHJciUUPE-q2SMcd8zX2FMOXGT2RJfng/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMeanCurvature) are neatly covered, I unfortunately could not find the same descriptions for sulcal depth. Any clarifications would be greatly appreciated.
Thank you in advance!
Kind regards Linn Norbom
External Email - Use Caution
OK perfect, thank you so much for the clarification!
Kind regards Linn
________________________________ 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: 06 February 2024 15:35:16 To: Freesurfer support list Subject: Re: [Freesurfer] calculation of sulcal depth
Hi Linn
The text you cite is how we measure it. It is the signed distance each points moves to get from the white to the inflated surface, where outwards movement is positive (along the surface normal direction) and inwards distance is negative.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Linn Christin Bonaventure Norbom Sent: Tuesday, February 6, 2024 8:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] calculation of sulcal depth
External Email - Use Caution Dear experts,
I am assessing different morphological aspects of the cortex including sulcal depth but am struggling to understand how this is calculated in FreeSurfer. I see that a previous correspondence (https://secure-web.cisco.com/17UFKrNEsAz2sbufihMcQDONUJK07Rabz1hBwgQnCV0_4Da...) points to this being described on page 199 within the “Cortical surface-based analysis II” – paper, by Fischl et al. but to my understanding it only describes the inflation process. Is it so that as concave areas like sulci move outward, while convex areas like gyri move inward during this process, this movement is somehow quantified and used to calculate sulcal depth? I also see a previous article stating that “..Freesurfer's sulcal depth measurement measures how far a vertex moves during an inflation operation”, also referencing the same Fischl paper.
While other folding measures like LGI (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/15zaRhNC9Gz2IJ5YjV7AwLqUoAjKhY6J96nEnBm8vCDW7OB...https://secure-web.cisco.com/1rZbD04F-L_WBb_-7dP8B298OK6uZo1zDlLneMBGyND_ivL2gPkiZTug0WyglfVkOxxiC02F2Fh9blwiaSive2lw9mQNXXar3KvM6viLVnbE0k8g7scdmmyXJnbPb5wzV7dorN16_yT8hpRYKkSnOgVJPTiYFr6imCXCw0oqSa3vw69icYlZlp0nrJEZ8CQI6THyg7T7c18tXbLwhC255w6lGcKFdcqQrkDtTxdDJ2m2rKsF8kH0AyALHcPwzFqoW5lVOAgzmbhZXo18NET-ucEVyQLZkek29qz2zU84XKJGF_9yRPSlYxRMomM5dW00gbbDpAYbhEk1jwn-WXxTb6w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI and curvature (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-7akPiNVTlNC9KxMTovd50a0rRROLiMJCFH9KZ2F4r4_Xh...https://secure-web.cisco.com/1bY39JsrtiDKpPFJNg4aHhIchmGuug1PSRGvTczzLFMkNC8ifemRnYXnUDdmvRVVZ4BQmPxQvIJYXoUo14A2_GWqoJNuEnMk1x13Nj6Nu8dkE12w8VdN62Wvy5k2ihHSWjarOV9aYXxP7z56hbzOv-OIIfyD4jdXX65nYsgl0gy63HZMpxvtIe7E4aREI07xP6OJiWKOkIBQcg4rhaXvSYofqQl930k1EpdawV8TMZBGr7tPI8p4Q8x99pg9LtQAkPs9_1zpMUeiIRrajetzyPwuc597BofExcrVipWR3eBC0nVk_aC7UjmoHJciUUPE-q2SMcd8zX2FMOXGT2RJfng/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMeanCurvature) are neatly covered, I unfortunately could not find the same descriptions for sulcal depth. Any clarifications would be greatly appreciated.
Thank you in advance!
Kind regards Linn Norbom
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce R.,PHD -
Linn Christin Bonaventure Norbom