Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

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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.commailto:sallyagrace@gmail.com (preferred) | sgrace@swin.edu.aumailto: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.comhttp://www.jeiglesias.com

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

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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/HippocampalSubfieldsAndNucleiOfAmy...https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). Can the scripts be adapted to Freesurfer v5.3?

Thanks in advance,

Sally.

HippocampalSubfieldsAndNucleiOfAmygdala - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu

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