Thanks Eugenio,

I'll do that.

Again very much appreciate your guidance.

Cheers

Erik

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: 08 December 2017 16:46
To: Freesurfer support list
Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation

Command looks good! But I’d replace HippoAMYT1andT2 by something that reflects the fact that you’re using a FLAIR scan ;-)

Regarding the 2^nd question: try running segmentHA_T2.sh. If it’s not there, you’ll need a more recent (dev) version.

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon@rcsi.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 8 December 2017 at 14:41
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation

Hi Eugenio,

Thanks so much for you input. I think I get it now. so I will run the following to get a multispectral segmentation using both T1 and T2Flair?

segmentHA_T2.sh /projects/freesurfer/subjects/sub001 /projects//freesurfer/subjects/sub001_T2.nii.gz HippoAMYT1andT2 1 sub001

Just as a quick aside, I'm not sure if my FS 6.0 contains the necessary options to run the Amygdala stuff. Is there an easy way I can check this and if I dont have the correct tool can I simply ad that to my FS build?

Thanks again and as always, very much appreciate your help.

Cheers

Erik

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: 08 December 2017 14:29
To: Freesurfer support list
Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation

Hi Erik,

You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multiple segmentations at different hierarchies, but only one text file with all the volumes.

Regarding your old 6.0 measures: they’re safe because they used the suffix v10, and the new ones use the suffix v20

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon@rcsi.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 8 December 2017 at 14:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] new Amygdala and Hippocampus segmentation

Hi FS experts,

I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run?

for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ?

segmentHA_T2.sh  subject001  subject001_Flair.nni.gz   T1andFlair  USE_T1  /subject001

Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir?

Thanks for any help you can provide .

Erik

Erik O'Hanlon
Postdoctoral researcher

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE