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.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?

External Email - Use Caution

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?

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/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

External Email - Use Caution

Hi Eugenio and experts,

We are doing a multi-site data analysis comparing groups cross-sectionally. Most data that we will input for the segmentHA_t1.sh analysis has been pre-processed cross-sectionally in FS5.3 (recon all).

About 10% of the data has been pre-processed in FS5.3 longitudinally as we are using only the latest assessment point time 3 (e.g., subject name is subjectID_3.long.subjectid).

Are volumes for one subject identical whether processed cross-sectionally and longitudinally or does the longitudinal processing affect the volumes? We don't know if we have to rerun the preprocessing of this via the FS5.3 cross section pipeline and are looking forward to hearing your advice.

Thanks in advance,

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: Sally Grace Sent: Thursday, 14 June 2018 2:47:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

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?

External Email - Use Caution

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?

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/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