There is an automatic topology fixer in the stream. While sometimes it
fixes an topo error properly, it does not always do so, so you will need
to see whether it has fixed is or not. It is the white surface that is
in error, which is created from the wm.mgz (or filled.mgz), so you will
need to fix one of those volumes.
On 12/14/2021 5:26 AM, Nilab Nasrullah wrote:
External Email - Use Caution
I am using freesurfer 7.1.This particular subject's segmentation
didn't include the cerebral cortex of the occipital lobe (see image
1). Although I can see there are defects in that specific place, there
are also defects in other places (see atttached images). I have
followed the instructions on how to correct topological errors but
that doesn't seem to help much since it is the grey matter that is not
included in the segmentation.
Can you provide me with some instructions on how to fix these defects?
Thanks,
Nilab
------------------------------------------------------------------------
*From:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Sent:* 11 December 2021 00:24
*To:* Nilab Nasrullah <nilab.nasrul...@stud.ki.se>;
freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Help
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 <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah <nilab.nasrul...@stud.ki.se>
<mailto:nilab.nasrul...@stud.ki.se>; 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 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:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@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:
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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/När du skickar e-post till Karolinska Institutet (KI) innebär detta
att KI kommer att behandla dina personuppgifter. /Här finns
information om hur KI behandlar personuppgifter
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/När du skickar e-post till Karolinska Institutet (KI) innebär detta
att KI kommer att behandla dina personuppgifter. /Här finns
information om hur KI behandlar personuppgifter
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