Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain

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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:

[cid:b9b7dd97-cf68-49bf-bf8a-a9633f34062a]

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

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Dear FreeSurfer experts,

I am fixing the error generated by recon-all. Please see the capture below:

[cid:image001.png@01D9C53D.E8D6F9E0]

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

[cid:image002.png@01D9C53D.E8D6F9E0]

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

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