External Email - Use Caution        

Hi Eugenio, 

Great. We have already run our subjects through recon-all for FS5.3. EG. recon-all -s [subjects_dir]

We have two dev versions of freesurfer installed on our server: freesurfer/devel-20180612 and freesurfer/devel-20171013. Does it make any difference if we use either version? We aim to use freesurfer/devel-20180612 as it is the latest. 

We have T1 crossectional data processed using FSV5.3 recon-all. Can I bypass running recon-all again and directly perform the segmentation via the command below (without typing in recon-all at the start of the terminal?):

segmentHA_T1.sh [SUBJECTS_DIR]

Kind regards,
Sally. 



Sally Grace
BSc (Hons), PhD Candidate.
Centre for Mental Health
Faculty of Health, Arts and Design | Swinburne University of Technology
Hawthorn, 3122

(03) 9214 8415

sallyagrace@gmail.com (preferred) | sgrace@swin.edu.au


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
Sent: Wednesday, 6 June 2018 6:09:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?
 

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Dear Sally,

You will need to download the development version to access this functionality.

However, if you have already run your subjects through recon-all with FS5.3, you can directly call segmentHA_T1.sh/ segmentHA_T2.sh/ segmentHA_T1_long.sh in the dev version (no need to run recon-all again with dev).

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sally Grace <sgrace@swin.edu.au>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 6 June 2018 at 03:16
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

 

        External Email - Use Caution        

Hi there, 

 

I wish to segment amygdala nuclei in Freesurfer Version 5.3, is it possible? I can find documentation only for Freesurfer version 6.0 here (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). Can the scripts be adapted to Freesurfer v5.3?

 

Thanks in advance, 

Sally. 

Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal) This functionality has been available in the development version of FreeSurfer since August 31st 2017