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Dear Bruce,
Your kind attention is highly appreciated!
I have shared the folder with you, please find the link in your inbox.
Thanks a lot again!
Best regards,
Krystal
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Sent: 03 August 2023 11:23:42
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain
External Email - Use Caution
It is impossible to diagnose without seeing the data. Can you upload it
somewhere we can take a look?
Cheers
Bruce
On Aug 2, 2023, at 10:24 PM, Krystal Xiwing Yau <kryst...@hku.hk> wrote:
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Dear Bruce,
Thank you very much for your advice.
I am concerned about the large area of the brain not being segmented. The wm
intensity ranged from 0 to 110, it goes up as it is closer to the white matter.
I literally added some control points on my end and rerun the command recon-all
-autorecon2-cp -autorecon3 -s <subjectID>. The surfaces are not extending to
the temporal lobe. Please kindly refer to the image below for your reference:
<pastedImage.png>
The problem is still there after several trials and following tutorials. Would
you please further suggest how to fix this?
Thank you very much.
Best regards,
Krystal
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Sent: 03 August 2023 00:36:11
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain
External Email - Use Caution
Hi Krystal
What is the intensity of the white matter in that region? It looks like a
topological defect but you have to figure out why it occurred. If the wm in
that region is significantly < 110 then control points might help
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Krystal Xiwing Yau
Sent: Tuesday, August 1, 2023 9:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain
External Email - Use Caution
Dear FreeSurfer experts,
I am fixing the error generated by recon-all. Please see the capture below:
<image001.png>
Fig.1 Under-segmentation of white and pial surfaces still not fixed after
running the command with the flags -autorecon2-cp -autorecon3 for the subject
<image002.png>
Fig.2 The same image for the subject, with the visible wm.
The tutorial
<https://secure-web.cisco.com/1eFs9sHrAZSKhe4nUQhj-OHr9PCuaQnsYS1AVa0FxCl5k_hKYiMAFogtkur4MUZRpuU6ZPLP7XgTJZukr0-4EWM9hEOjYwqevzL5TjCE12141mhqD2o9IYCXFtIbuC71UTq-5Ecp7KeiJgjeM3Ld7Ptg4aYou6HO8Cfg-5k4gzm5fXh0NEzEg10tuQUE8JOaG9wEkJQi4d355pGuStT2lFCDNMBNEk3GFXGCyho0K0Hs3g3KAPTLQNKnPtsoPIRyVPpYEcolFLFbSKEZjdvFLl0qhZZ3aeM43TZoeRzzAYlUE2GaMV8F0EpfaSn3zTGUWThN0RWPjZMBcwtpAVC-XnA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FControlPoints_freeview%2F>
from the FsTutorial indicated that adding control points to the white matter
area only. Moreover, the pial surface expends from the white surface. Thus, it
is not possible to add control points on the cortex. Would somebody can help
with fixing such error, please?
Thank you very much!
Regards,
Krystal
Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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