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:
External Email - Use Caution
Sure. See attached.
//Nilab
------------------------------------------------------------------------
*From:* Douglas N. Greve <[email protected]>
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah <[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?
On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:
External Email - Use Caution
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:* [email protected]
<mailto:[email protected]>
<[email protected]>
<mailto:[email protected]> on behalf of Douglas
N. Greve <[email protected]> <mailto:[email protected]>
*Sent:* 29 November 2021 04:01
*To:* [email protected]
<mailto:[email protected]>
<[email protected]> <mailto:[email protected]>
*Subject:* Re: [Freesurfer] Help
Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
External Email - Use Caution
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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