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:
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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:
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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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Wednesday, October 7, 2020 10:17 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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.
- FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Platform: Ubuuntu 14.04
3) recon-all.log: see attached
Best Regards,
Kazuki Sakakura
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Douglas N. Greve