External Email - Use Caution
Dear FreeSurfer experts,
I am fixing the error generated by recon-all. Please see the capture below:
[cid:a7289c63-1b2b-407c-9dec-a9ff5e082daa]
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:baf96016-01d2-4d50-ac8e-ce6067c1dec6]
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.
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
External Email - Use Caution
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
Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
External Email - Use Caution
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
External Email - Use Caution
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
Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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 krystaly@hku.hk wrote:
External Email - Use Caution
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-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
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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16Qef0jjgi4xpYbXes5eGbA6ne1cIQ0odlcDhjCs0F_7NNS...
External Email - Use Caution
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-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 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 krystaly@hku.hk wrote:
External Email - Use Caution
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-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
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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/17QdghzbY9vyVqrXBoEuWR2d3FBDS3jBWFe-Q49F9g_A0Kq...
External Email - Use Caution
Can you send me the voxel coordinates of a point that you think should be included but is not?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Thursday, August 3, 2023 12:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@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 <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@MGH.HARVARD.EDUmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pNxE-psxiMeEd3FpDq1t7HOboaOszxnMI9-hfS0hU1Lw6P...
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce R.,PHD -
Krystal Xiwing Yau