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

[Fischl, Bruce R.,PHD]

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Can you send me the voxel coordinates of a point that you think should be 
included but is not?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Thursday, August 3, 2023 12:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain


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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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto: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


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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 
mailto: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 . The surfaces are not extending to 
the temporal lobe. Please kindly refer to the image below for your reference:





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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto: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


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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
 
mailto: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


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Dear FreeSurfer experts,



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




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


Fig.2 The same image for the subject, with the visible wm.



The tutorial 

  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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Re: [Freesurfer] Fw: cortical boundary and center of gravity

[alexandra.ko...@uksh.de]

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Dear Douglas,


If I have the distance between the nearest point on the white surface and the 
center of gravity ( this is d1), and the thickness of each point (d2), then I 
can sum d1+d2 and the result is what I need.


Is it possible to extract d1 and d2, as described above?


Really appreciate your kind response.


Alexandra




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 01 August 2023 15:58:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: cortical boundary and center of gravity

Achtung, externe Mail!

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If I understand correctly, you want to compute the distance between a given 
point (however you compute it) and the nearest(?) point on the white surface?

On 7/28/2023 6:04 AM, alexandra.ko...@uksh.de 
wrote:

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Dear Freesurfer expert,

Please receive my email as a kind reminder of my previous one: Can I extract 
the cortical boundary as a spatial series and the center of the mass in the 
grey matter segmented images using the FreeSurfer? Can you please let me know 
how to?

Many thanks in advance,
Dr. -Ing. Alexandra Korda

Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck
Tel.: +49 451 500-98715
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From: Korda, Alexandra
Sent: 25 July 2023 08:36:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical boundary and center of gravity


Dear Freesurfer expert,


Please receive my email as a kind reminder of my previous one: Can I extract 
the cortical boundary as a spatial series and the center of the mass in the 
grey matter segmented images using the FreeSurfer? Can you please let me know 
how to?


Many thanks in advance,

Dr. -Ing. Alexandra Korda

Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck
Tel.: +49 451 500-98715
alexandra.ko...@uksh.de I MailScanner has detected 
a possible fraud attempt from "secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/12zcjBKYc-OjKVfcdvvhzgCqQIo0A7dErz95lijPbD4hTh-GIiaJ4K5eh-AaeSbeuT4Ksc2dmPXmr9OwaXL1jnNEr9QxDGs20vyNNpWy15vS37E6h7gSyKmLRoOvcgy0JjTHUfhn4_YaJKT0O7oheOEt5cUCS6pz68cWHbo8CCBtNgkn5S-L4PV0Y3_3kYvJKEI0OrGMlmtwAfUfYiRWz542vFDR5Zr0LWgg7a9434S9XpqH1ydkBHBKczz5xcEa4NzeMyXiWcGNug6OTULXqbAvV4rEoZwOVTtwu3-KrynTDb1q92zsenT1HMxNIbrhVCZ5Rj6NuBe_xuryJ4s3AmA/http%3A%2F%2Fwww.zip.uksh.de

[Freesurfer] using synthsr with HCP Pipeline

[KennethSPrice]

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Hello all,

I am currently struggling through the HCP Pipeline! I want to use clinical 
scans processed with synthsr in the HCP Pipeline.
1.) Is this even possible?
2.) Is there a way to get a T2 output with synthsr?
3.) In lieu of the HCP Pipeline, could you use SythSR scans with the HCP 
Database to do a normal group analysis?

Thanks,
Ken___
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Re: [Freesurfer] using synthsr with HCP Pipeline

[Glasser, Matt]

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That’s not easy to do out of the box, because you would need to run SynthSR 
before PreFreeSurfer, when normally you do the reverse.  Not having T2w scans 
just means you would need to enable legacy mode options.

I have some code that imports a SynthSR result into HCP Pipeline structures, 
though SynthSR is rapidly changing and each time it changes I have to update 
that import code.  Perhaps I can share it once things have stabilized.

Matt.

From:  on behalf of KennethSPrice 

Reply-To: Freesurfer support list 
Date: Thursday, August 3, 2023 at 12:30 PM
To: Freesurfer support list 
Subject: [Freesurfer] using synthsr with HCP Pipeline



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Hello all,

I am currently struggling through the HCP Pipeline! I want to use clinical 
scans processed with synthsr in the HCP Pipeline.
1.) Is this even possible?
2.) Is there a way to get a T2 output with synthsr?
3.) In lieu of the HCP Pipeline, could you use SythSR scans with the HCP 
Database to do a normal group analysis?

Thanks,
Ken


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[Freesurfer] freeview (visualize pial and white surface)

[DS]

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Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


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Re: [Freesurfer] freeview (visualize pial and white surface)

[Wang, Ruopeng]

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Would it be possible to send us the two surface files?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)


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Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.


../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.


But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized.


Do you have any thoughts about this issue? Thank you so much for any 
suggestions.

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