Re: [Freesurfer] Amygdala subfields segmentation

2018-09-12 Thread Iglesias Gonzalez, Eugenio 
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ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Tuesday, September 11, 2018 5:59:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Amygdala subfields segmentation


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Hi Eugenio,


Where can I find the link for download the latest dev version?


The latest version is this?:

freesurfer-darwin-OSX-ElCapitan-dev.tar.gz


Thanks in advance,


Best,


El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio 
(mailto:e.igles...@ucl.ac.uk>>) escribió:

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Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Sent: Tuesday, September 11, 2018 12:20:55 PM
To: Freesurfer support list
Subject: [Freesurfer] Amygdala subfields segmentation


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Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command " 
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" 
but freesurfer gave to me this error command not found.


However, when I use the command that segment only the hippocampal subfields 
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

--
Miguel Ángel Rivas Fernández
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--
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Re: [Freesurfer] Amygdala subfields segmentation

2018-09-11 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hi Eugenio,


Where can I find the link for download the latest dev version?


The latest version is this?:

*freesurfer-darwin-OSX-ElCapitan-dev.tar.gz*


Thanks in advance,


Best,


El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio (<
e.igles...@ucl.ac.uk>) escribió:

> External Email - Use Caution
>
> Dear MA
> Please download the latest dev version and the command will be there
> Cheers
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández 
> *Sent:* Tuesday, September 11, 2018 12:20:55 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Amygdala subfields segmentation
>
>
> External Email - Use Caution
>
>
> Hi Freesurfer developes,
>
> I am trying to execute the hippocampal and amygdala segmentation command "
> segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1
> [SUBJECTS_DIR]" but freesurfer gave to me this error
> *command not found. *
>
>
> However, when I use the command that segment only the hippocampal
> subfields (recon-all -s  -hippocampal-subfields-T2  of additional scan> ) I don´t have any problem.
>
>
> What would be the reason?
>
>
> Thanks in advance.
>
>
> Best,
>
> --
> *Miguel Ángel Rivas Fernández*
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Amygdala subfields segmentation

2018-09-11 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Tuesday, September 11, 2018 12:20:55 PM
To: Freesurfer support list
Subject: [Freesurfer] Amygdala subfields segmentation


External Email - Use Caution

Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command " 
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" 
but freesurfer gave to me this error command not found.


However, when I use the command that segment only the hippocampal subfields 
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

--
Miguel Ángel Rivas Fernández
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Amygdala subfields

2016-10-31 Thread Dorit Kliemann 
to clarify: the amygdala subregion atlas is built and will be released early 
2017.

Dorit

On Oct 31, 2016, at 11:46 AM, Dorit Kliemann  wrote:

> Hi Sascha,
> yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
> subfields . Its currently being tested and to be implemented (hopefully) 
> soon. Stay tuned. 
> 
> Dorit
> 
> 
>> From: "sf" 
>> Subject: [Freesurfer] Amygdala subfields
>> Date: 31 October 2016 at 15:13:21 GMT
>> To: "'Freesurfer support list'" 
>> Reply-To: Freesurfer support list 
>> 
>> Hi all, is there any possibility to segment amygdala subfields with 
>> freesurfer? Similar to the hippocampal subfields segmentation?
>> Cheers - Sascha
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 



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Re: [Freesurfer] Amygdala subfields

2016-10-31 Thread Dorit Kliemann 
Hi Sascha,
yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
subfields . Its currently being tested and to be implemented (hopefully) soon. 
Stay tuned. 

Dorit


> From: "sf" 
> Subject: [Freesurfer] Amygdala subfields
> Date: 31 October 2016 at 15:13:21 GMT
> To: "'Freesurfer support list'" 
> Reply-To: Freesurfer support list 
> 
> Hi all, is there any possibility to segment amygdala subfields with 
> freesurfer? Similar to the hippocampal subfields segmentation?
> Cheers - Sascha
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 


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Re: [Freesurfer] Amygdala subfields

2014-11-24 Thread Eugenio Iglesias 
Hi Stefano,
we are working on an algorithm to segment the nuclei, but unfortunately I do 
not think it is going to be released any time soon.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: std...@virgilio.it
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, November 24, 2014 3:42:05 AM
Subject: [Freesurfer] Amygdala subfields


Dear all, 


is the amygdala subfields segmentation available or you are working on it? 


Thanks, 




Stefano 
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