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.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.

 

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!

 

  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:
    1. recon-all -autorecon1 -s <subj_id> -i <mp2rage_input> 
    1. check and verify skull strip quality
    1. 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.

 

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