External Email - Use Caution
Hi Freesurfers,
I have a question reagrding to how the pial surface is generated. For an oversimplified description, I assume each subject's pial surface was initially created with a spherical shaped 3D-topology model. Then each verticie on the sphere is assigned to specific location of the pial surface to cover the subject's brain. If that is the case, then I don't understand the result illustrated below in the figure. The figure is showing anatomical T1w image overlay with left and right pial surface from recon-all (command used at the end), while the red cross is targeting a pial surface located within cortical region. Although there is some mis-segmentation error nearby, I don't see the pial surface inside of the cortical region is connecting to any outer surface when I move the image slice back and forth. Is this allowed or even possible if the initial spherical surface can generate such discrete surface that is disconnected from the whole outer brain region?
[cid:20a64222-bc84-4c74-9935-ffd295eac833]
Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance!
1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Ubuntu 24.04.2 LTS 3. uname -a: Linux hawaii 6.11.0-26-generic #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4. Command and steps used for recon-all: * recon-all -autorecon1 -s <subj_id> -i <mp2rage_input> * check and verify skull strip quality * recon-all -autorecon2 -autorecon3 -s <subj_id>
Best,
Yujia Huang
Research Engineer
Advanced Imaging Research Center
UT Southwestern Medical Center
2201 Inwood Rd.
Dallas, TX, USA, 75390
Office: 214.645.5241
Pronouns: He, Him, His
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
I'm not sure exactly what you are ttalking about. Can you draw a circle around the point in the image? The pial surface starts from the white surface and then it is pushed outward (this is not the process you describe). It should all be connected.
On 7/27/2025 10:13 PM, Yujia Huang wrote:
External Email - Use Caution
Hi Freesurfers,
I have a question reagrding to how the pial surface is generated. For an oversimplified description, I assume each subject's pial surface was initially created with a spherical shaped 3D-topology model. Then each verticie on the sphere is assigned to specific location of the pial surface to cover the subject's brain. If that is the case, then I don't understand the result illustrated below in the figure. The figure is showing anatomical T1w image overlay with left and right pial surface from recon-all (command used at the end), while the red cross is targeting a pial surface located within cortical region. Although there is some mis-segmentation error nearby, I don't see the pial surface inside of the cortical region is connecting to any outer surface when I move the image slice back and forth. Is this allowed or even possible if the initial spherical surface can generate such discrete surface that is disconnected from the whole outer brain region?
Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance!
- Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
- Platform: Ubuntu 24.04.2 LTS
- uname -a: Linux hawaii 6.11.0-26-generic #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
- Command and steps used for recon-all:
- recon-all -autorecon1 -s <subj_id> -i <mp2rage_input>
- check and verify skull strip quality
- recon-all -autorecon2 -autorecon3 -s <subj_id>
Best,
**
*Yujia Huang*
Research Engineer
*/Advanced Imaging Research Center/*
UT Southwestern Medical Center
2201 Inwood Rd.
Dallas, TX, USA, 75390
Office: 214.645.5241
Pronouns: He, Him, His
UTSouthwestern
Medical Center
The future of medicine, today.
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
External Email - Use Caution
Hi Douglas,
Sorry for the confusion. I have drawn the arrow pointing at the point in the attached image. From the sag, cor and transverse view of that point, it doesn't connect to the outer pial surface, is this possible?
Thanks!
Best,
Yujia
________________________________ From: Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, July 31, 2025 8:41 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Discrete pial surface
External Mail This email originated from outside of UT Southwestern. Please be cautious. Report Suspicioushttps://secure-web.cisco.com/1vjKcYogRLwJMd6yyHYOQA9yd7kB_8kdewK0BlCaTRD2ak8BVAeeODUEeeR0Xd_E2HME5yh_iboP0QzU3yxzwWRDSOu94liCy_Kcu8pRiXyn9PyGOno7tnlCN90AneJKjwmS9waN4VRt2MwgWWTdOQyOI8IcGdEubGMQyFtyC-wkHkW-TjUsyfw3XgkxZGYsUQ3XXskC0ELpti7vELIFYAO6SIAV6qSmyVHF6SSWbYHavnzSqHIToP7NVSq6h2v38dZnWsh8E4EN1Hj610feh5XWEpYZ5Zd3qeBnMMUqV3Ijj5JLouhu1lqjopw5OjYP3ns1XnHZDx0XQk_DmT78T0Q/https%3A%2F%2Fus-phishalarm-ewt.proofpoint.com%2FEWT%2Fv1%2FMznTZTSvDXGV0Co%21VbxNmfZY6lqX6REPZ5P4LXaWbjIDc17XMxdU30Ok57iRozQkSedZSmK9DWiy6LkmQ_F7nFKyYkaUFu6icZPdSqjoZFvakiLcnq4-_FYpQxAVqapzJErW%24
I'm not sure exactly what you are ttalking about. Can you draw a circle around the point in the image? The pial surface starts from the white surface and then it is pushed outward (this is not the process you describe). It should all be connected.
On 7/27/2025 10:13 PM, Yujia Huang wrote: External Email - Use Caution Hi Freesurfers,
I have a question reagrding to how the pial surface is generated. For an oversimplified description, I assume each subject's pial surface was initially created with a spherical shaped 3D-topology model. Then each verticie on the sphere is assigned to specific location of the pial surface to cover the subject's brain. If that is the case, then I don't understand the result illustrated below in the figure. The figure is showing anatomical T1w image overlay with left and right pial surface from recon-all (command used at the end), while the red cross is targeting a pial surface located within cortical region. Although there is some mis-segmentation error nearby, I don't see the pial surface inside of the cortical region is connecting to any outer surface when I move the image slice back and forth. Is this allowed or even possible if the initial spherical surface can generate such discrete surface that is disconnected from the whole outer brain region?
[cid:part1.gtwr0c6Q.L0dZcX10@mgh.harvard.edu]
Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance!
1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Ubuntu 24.04.2 LTS 3. uname -a: Linux hawaii 6.11.0-26-generic #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4. Command and steps used for recon-all: * recon-all -autorecon1 -s <subj_id> -i <mp2rage_input> * check and verify skull strip quality * recon-all -autorecon2 -autorecon3 -s <subj_id>
Best,
Yujia Huang
Research Engineer
Advanced Imaging Research Center
UT Southwestern Medical Center
2201 Inwood Rd.
Dallas, TX, USA, 75390
Office: 214.645.5241
Pronouns: He, Him, His
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1unB4llcbJBeprFiE3bgvQ-jqUDqy6CDECdFMe9xl0E59Na...https://secure-web.cisco.com/1YNSj54F_y5xn8zcAIPw92WBvEEIrlOunTXFmPPg-b1K_sCdJKiragNp1YQe7OTJxEbHkLYgSJpcm_n3fixAZOzX5yk6fVQ5Y9vZJxBqhguSJEWiqIaDLYdohkhBStcmj-g7JXaUhHE2ADlbqNIHualOoOyMKpjnbKu9Hs0BP33TEHwnNr0SBJytTQOaijfH6D3N1Wq0itDNhiXeInwPqYLdSpSEbU05-xfqPL4UDzNrYgEHtUehJl4XLqXQy8i0S722iFvsfsHiRSS5Ir_K6dM6Of8jc9ebA8lrunsw37YXdqmGZcrmuKtix1yR6hm68YT1_5z0pmm5lWCSykoBl0Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F__;!!MznTZTSvDXGV0Co!DDd3QKxI06wRNisQNTe9qjDk7GHGGwyv8tCKIcOfD0e-Wkg_SnjNwrHoaw-af4JAkVeqZ1snAbfCEFOSbQC8WrRHuVJ_Ifl3Ug$
No. If you scroll through the slices it will attach at some point. The topology of a slice of a topologically-spherical surface is a set of closed curves that don't necessarily connect in the slice, but they will in 3D
Cheers Bruce
From: Yujia Huang Yujia.Huang@UTSouthwestern.edu Sent: Wednesday, August 6, 2025 10:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Discrete pial surface
External Email - Use Caution Hi Douglas,
Sorry for the confusion. I have drawn the arrow pointing at the point in the attached image.
From the sag, cor and transverse view of that point, it doesn't connect to the outer pial surface, is this possible?
Thanks!
Best,
Yujia
________________________________ From: Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Thursday, July 31, 2025 8:41 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Discrete pial surface
External Mail This email originated from outside of UT Southwestern. Please be cautious. Report Suspicioushttps://secure-web.cisco.com/1vjKcYogRLwJMd6yyHYOQA9yd7kB_8kdewK0BlCaTRD2ak8BVAeeODUEeeR0Xd_E2HME5yh_iboP0QzU3yxzwWRDSOu94liCy_Kcu8pRiXyn9PyGOno7tnlCN90AneJKjwmS9waN4VRt2MwgWWTdOQyOI8IcGdEubGMQyFtyC-wkHkW-TjUsyfw3XgkxZGYsUQ3XXskC0ELpti7vELIFYAO6SIAV6qSmyVHF6SSWbYHavnzSqHIToP7NVSq6h2v38dZnWsh8E4EN1Hj610feh5XWEpYZ5Zd3qeBnMMUqV3Ijj5JLouhu1lqjopw5OjYP3ns1XnHZDx0XQk_DmT78T0Q/https%3A%2F%2Fus-phishalarm-ewt.proofpoint.com%2FEWT%2Fv1%2FMznTZTSvDXGV0Co%21VbxNmfZY6lqX6REPZ5P4LXaWbjIDc17XMxdU30Ok57iRozQkSedZSmK9DWiy6LkmQ_F7nFKyYkaUFu6icZPdSqjoZFvakiLcnq4-_FYpQxAVqapzJErW%24
I'm not sure exactly what you are ttalking about. Can you draw a circle around the point in the image? The pial surface starts from the white surface and then it is pushed outward (this is not the process you describe). It should all be connected. On 7/27/2025 10:13 PM, Yujia Huang wrote: External Email - Use Caution Hi Freesurfers,
I have a question reagrding to how the pial surface is generated. For an oversimplified description, I assume each subject's pial surface was initially created with a spherical shaped 3D-topology model. Then each verticie on the sphere is assigned to specific location of the pial surface to cover the subject's brain. If that is the case, then I don't understand the result illustrated below in the figure. The figure is showing anatomical T1w image overlay with left and right pial surface from recon-all (command used at the end), while the red cross is targeting a pial surface located within cortical region. Although there is some mis-segmentation error nearby, I don't see the pial surface inside of the cortical region is connecting to any outer surface when I move the image slice back and forth. Is this allowed or even possible if the initial spherical surface can generate such discrete surface that is disconnected from the whole outer brain region?
[cid:image001.png@01DC06BE.A6D608F0]
Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance!
1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
1. Platform: Ubuntu 24.04.2 LTS
1. uname -a: Linux hawaii 6.11.0-26-generic #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
1. Command and steps used for recon-all:
* recon-all -autorecon1 -s <subj_id> -i <mp2rage_input>
* check and verify skull strip quality
* recon-all -autorecon2 -autorecon3 -s <subj_id>
Best,
Yujia Huang
Research Engineer
Advanced Imaging Research Center
UT Southwestern Medical Center
2201 Inwood Rd.
Dallas, TX, USA, 75390
Office: 214.645.5241
Pronouns: He, Him, His
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu
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freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce R.,PHD -
Yujia Huang