[Freesurfer] Support for GPU on Freesurfer

[Camargo, Aldo]

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Hi there,

I was wondering if there is support for GPU on FreeSurfer. I really would like 
to use it on GPU because is taking 9 hours per subject to recon-all.

Thanks a lot and have a nice day,

Aldo Camargo
Senior Postdoctoral Fellow at the University of Maryland, Baltimore


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[Freesurfer] Temporal lobe mask

[Camargo, Aldo]

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Hi there,

I would like to know where I can find a mask in MNI space for the temporal lobe.

Thanks a lot in advance for your help,

Aldo Camargo

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Re: [Freesurfer] How to cite Freesurfer

[Camargo, Aldo]

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Thanks a lot Alison,

Aldo Camargo

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Player, Allison A. 
Stevens 
Sent: Friday, September 3, 2021 5:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to cite Freesurfer

Hi Aldo,
Feel free to take whatever is relevant from this wiki for your citation:
https://secure-web.cisco.com/1d01SsF_adkbUpXR6F6HhdsS3kgH0LfTZ1zw2ejAxmLDRLG8aKQoTz6P3HTaTvj6NE2KUlhFVor-Hmddo00DEnhu1h9fawfA66PcVjsvHkjf_OQ9p3qWz4uctwSeRGQkppXazNhPL9oN04WglpyL9EXFO04iTjfC-YOPF6BdmbhMuxjtw1dOnllrVqF9qCoHvBluX0dn-mCZD8hgLmV_O4YNhsOkyGdPzjQgfecxFnU3mI0Vf4foSnbiyuje_hSk7MKXUl1-JdqbS_o7Hfrzm2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurferMethodsCitation<https://secure-web.cisco.com/1Nh7dNYkxwnevWpPmWPnfz-syTw0QKNB_oMYeBR5GNPpVsCH_EUWN0W7NqWVW2IBhc8uyJ-eRSQmXLTXkp4fAMUPWnFnz2I0hbZbmFXlbiWu-Tlmj0qVOmwy1imx801HIf8qn4UuVWjC9L07M_tUlguTt10KT0_OY2f5u5CTL9mcemJwDsyNhXC8djpKRib4WsfLavvk8ZMYAFQx81XmsHxE0qkC46mgZZzfJQi7MozDlpQICyfknL3ONLrzr0tMNew87h3Qf4MNjP6-R1-V38Q/https%3A%2F%2Fnam11.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFreeSurferMethodsCitation%26data%3D04%257C01%257Cacamargo%2540som.umaryland.edu%257Ce52f4b6b63984039463c08d96f1ecda3%257C717009a620de461a88940312a395cac9%257C0%257C0%257C637663000353548122%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DBTYOt4wc%252Fte6cyQ3CB3bMWGmlMDSecIU3EZnbVNlsF0%253D%26reserved%3D0>

Allison

On Sep 3, 2021, at 2:51 PM, Camargo, Aldo 
mailto:acama...@som.umaryland.edu>> wrote:


External Email - Use Caution


External Email - Use Caution

Hi Freesurfer group:

How should I cite freesurfer in my manuscript ?

Thanks a lot and have a nice day,

Aldo

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[Freesurfer] How to cite Freesurfer

[Camargo, Aldo]

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Hi Freesurfer group:

How should I cite freesurfer in my manuscript ?

Thanks a lot and have a nice day,

Aldo

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[Freesurfer] CSF file

[Camargo, Aldo]

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Hi Freesurfer experts:

I used recon-all all to in my MPRAGE image and I would like to know which file 
is the corresponding to the CSF (cerebral spinal fluid).
Also, which is the correct file to choose for the brain extracted image, 
because I see 2 files that can be:  T1.mgz, brain.mgz , which one is the 
correct ?
Also for GM the file is aparc+aseg.mgz the correct file ?

Thanks a lot and have a nice day,

Aldo

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Re: [Freesurfer] How to extract the GM and WM

[Camargo, Aldo]

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Hi Bruce,


I was wondering if there is way to continue the process to recon-all once I 
have done the recon-all with the option -autorecon1.

Thanks a lot,

Aldo


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Monday, May 24, 2021 10:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to extract the GM and WM


Hi Aldo



Usually we just run recon-all with -all instead of the individual -autorecon 
options. This will give you pretty much everything, including GM and WM



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Camargo, Aldo
Sent: Sunday, May 23, 2021 11:25 PM
To: Freesurfer support list 
Subject: [Freesurfer] How to extract the GM and WM



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External Email - Use Caution

Hi Freesurfer experts:



I want to extract the White Matter and the Gray Matter from a T1 image. I have 
extracted the brain by using the command:




recon-all with the option -autorecon1



Thanks a lot and have a nic day,



Aldo
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Re: [Freesurfer] How to extract the GM and WM

[Camargo, Aldo]

External Email - Use Caution

Thanks a lot Bruce,

Have a nice day,

Aldo

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: Monday, May 24, 2021 10:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to extract the GM and WM

Hi Aldo

Usually we just run recon-all with -all instead of the individual -autorecon 
options. This will give you pretty much everything, including GM and WM

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Camargo, Aldo
Sent: Sunday, May 23, 2021 11:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] How to extract the GM and WM


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External Email - Use Caution
Hi Freesurfer experts:

I want to extract the White Matter and the Gray Matter from a T1 image. I have 
extracted the brain by using the command:

recon-all with the option -autorecon1

Thanks a lot and have a nic day,

Aldo
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[Freesurfer] How to extract the GM and WM

[Camargo, Aldo]

External Email - Use Caution

Hi Freesurfer experts:

I want to extract the White Matter and the Gray Matter from a T1 image. I have 
extracted the brain by using the command:

recon-all with the option -autorecon1

Thanks a lot and have a nic day,

Aldo
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[Freesurfer] How to measure gray matter atrophy

[Camargo, Aldo]

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Hi Freesurfer experts:

Do you know how to measure the gray matter atrophy using FreeSurfer ? If so, 
please could you give me a tutorial to follow or some tips ?

Thanks a lot and have a nice day,

Aldo Camargo

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[Freesurfer] How can I get only aparc+aseg.mgz

[Camargo, Aldo]

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Hi Freesurfer experts:

I would like to get the aparc+aseg.mgz file, which options of recon-all should 
I use to get only that file. Because recon-all takes several hours.

Have a nice day,

Aldo

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Re: [Freesurfer] How to re-run recon-all

[Camargo, Aldo]

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Thanks a lot Bruce,

Aldo

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Friday, August 28, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] How to re-run recon-all


Hi Aldo



You should be able to use recon-all -make all … to run anything that did not 
complete. You might have to specify the -no-isrunning (or something like that) 
flag if it didn’t terminate cleanly



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Camargo, Aldo
Sent: Friday, August 28, 2020 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to re-run recon-all



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Hi Freeserufer experts:



By mistake I cancel the recon-all when it was about 3 hours of processing. 
There is a way to re-run the recon-all and that continues where it was stopped ?



Thanks a lot,



Aldo


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[Freesurfer] How to re-run recon-all

[Camargo, Aldo]

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Hi Freeserufer experts:

By mistake I cancel the recon-all when it was about 3 hours of processing. 
There is a way to re-run the recon-all and that continues where it was stopped ?

Thanks a lot,

Aldo

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Re: [Freesurfer] Run recon-all in MATLAB

[Camargo, Aldo]

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Hi Tim,

Thanks a lot for the quick response. I used system and it is working now 

Have a nice day,

Aldo

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: Wednesday, August 26, 2020 1:58 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Run recon-all in MATLAB

External Email - Use Caution

Hi Aldo,

What do you mean by 'still is not working'? What command did you run where 
(Matlab or Shell), and what was the error message?

I've had a quick look at that website, and from what I can tell it does not try 
to tell you how to run recon-all from Matlab. All it does is tell you how to 
get the FreeSurfer matlab functions (in $FREESURFER_HOME/matlab/) available in 
Matlab. E.g., after following that setup, you should be able to call 
'read_curv()' from Matlab to read morphometry data files like 
/surf/lh.area.

If you want to run recon-all (or any other system command) from Matlab, have a 
look at the Matlab 'system' function. I would recommend against it though.

Best,


Tim

> On August 26, 2020 at 7:10 PM "Camargo, Aldo"  
> wrote:
>
>
> External Email - Use Caution
>
> Hi Freesurfer community,
>
> Does someone know how to run recon-all  on MATLAB ? I tried the settings 
> suggest on 
> https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/FreeSurfer, but 
> still is not working;
>
> Thanks a lot in advance and have a great day,
>
> Aldo
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] Run recon-all in MATLAB

[Camargo, Aldo]

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Hi Freesurfer community,

Does someone know how to run recon-all  on MATLAB ? I tried the settings 
suggest on 
https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/FreeSurfer, but 
still is not working;

Thanks a lot in advance and have a great day,

Aldo
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[Freesurfer] How to run recon-all for different subjects and each subject with different sessions ?

[Camargo, Aldo]

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Hi Freesurfer experts,

I have a question:  How to run recon-all for different subjects and each 
subject with different sessions ?

Thanks a lot in advance and have a nice day,

Aldo
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[Freesurfer] Coregistration to MNI

[Camargo, Aldo]

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Hi Freesurfer experts,

I want to coregister a PET image to the MNI space, can I use mri_cvs_register ?

Thanks a lot,

Aldo Camargo
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[Freesurfer] Extract the cerebellum

[Camargo, Aldo]

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Hi Freesurfer experts,

I am trying to extract only the cerebellum and then save it to nii file. How 
can I do it with freesurfer ?

Thanks a lot and have a nice day,

Aldo

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