The data look pretty noisy in those images. My guess is that the WM is not getting segmented properly in that temporal area or there is an incorrectly fixed topology error. Try looking at the wm.mgz (or the filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to see where the defects are.
On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:
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Sure. See attached.
//Nilab
*From:* Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* 29 November 2021 15:40 *To:* Nilab Nasrullah nilab.nasrullah@stud.ki.se; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help Can you send them in plain, unzipped format?
On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:
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I am attaching a few screenshots of the segmented brain as zip-files. Hopefully, you can see the results. If not, let me know so I can send it to you in a different format.
Thanks, Nilab
*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:* 29 November 2021 04:01 *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] Help Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
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Hi,
I am editing subjects for a research project. After reconstruction, some parts of the brain are not included in the segmentation. Often, some parts of the temporal lobe and the cortex of the occipital lobe are not included. In some cases, the cortex of the frontal lobe is also affected.
I have tried using controls points, but the results don't change. I have also reconstructed them again, running autorecon1 and autorecon2&3 separately. I have lowered the watershed parameters, used the gcut command and edited manually after autorecon1 but in the end, the results don't vary significantly compared to running recon-all -all.
What can I do to include the missing parts?
Thanks, Nilab
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve