Those control points are still in gray matter.
Please remember to post to the list, thanks

On 10/9/2020 11:18 AM, Kazuki Sakakura wrote:

        External Email - Use Caution        

Thank you for continuously helping me.

With your comment, I performed to put some control points in WM (attached image).
However, the error was the same as before.

Like I said before, I performed infant recon-all and there were some slight defects in the medial temporal area (arrow).  Therefore I tried to modify the surface with control points.  Is this a reason why "autorecon2-cp -autorecon3" command had an error? If so, Do you know any ways to modify the surface for infant recon-all subjects?

Thank you.
Best Regards

Kazuki Sakakura

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, October 9, 2020 8:47 AM
To: Kazuki Sakakura <hg3544@wayne.edu>
Subject: Re: [Freesurfer] recon-all -s <subject> -autorecon2-cp -autorecon3 error
 
Those are all in gray matter. You need to make sure that they are all in voxels that are clearly white matter

On 10/8/2020 11:25 AM, Kazuki Sakakura wrote:

        External Email - Use Caution        

Thank you for replying.
 
I'm sure I put control points in WM as the attached picture.

I performed infant recon-all and there were some slight defects in the medial temporal area (arrow).  Therefore I tried to modify the surface with control points.  Is this a reason why "autorecon2-cp -autorecon3" command had an error? If so, Do you know any ways to modify the surface for infant recon-all subjects?

Thank you.
Best Regards

Kazuki Sakakura
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, October 7, 2020 10:17 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all -s <subject> -autorecon2-cp -autorecon3 error
 

[EXTERNAL]

I've never seen that one before. Can you post pictures of where you put the control points? Are you sure you put them in voxels that are clearly WM?

On 10/6/2020 4:33 PM, Kazuki Sakakura wrote:

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Hello FreeSurfer Developers, 

 

I'm attempting to compute recon-all after putting control point, but for some of my subjects I get the attached error when I run the recon-all -s <subject> -autorecon2-cp -autorecon3 command.


 

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.  

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 

2) Platform: Ubuuntu 14.04 

3) recon-all.log: see attached 


Best Regards,

Kazuki Sakakura



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