Thanks, Georgina!

So: the script to gather the volumes (quantifyHAsubregions.sh) is looking for lh.hippoSfVolumes-T1.v22.txt and rh.hippoSfVolumes-T1.v22.txt, but it seems that you have lh.hippoSfVolumes.txt and rh.hippoSfVolumes.txt instead. I am not sure how this happened…

One solution would be to rename the files in every subject’s “mri” directory, possibly with a script.

Another solution would be to edit quantifyHAsubregions.sh and replace:

  leftVolFile="$resultsDirectory/$subjectName/mri/lh.${prefix}Volumes-${suffix}.v22.txt"

  rightVolFile="$resultsDirectory/$subjectName/mri/rh.${prefix}Volumes-${suffix}.v22.txt"

By:

  leftVolFile="$resultsDirectory/$subjectName/mri/lh.${prefix}Volumes.txt"

  rightVolFile="$resultsDirectory/$subjectName/mri/rh.${prefix}Volumes.txt"

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Georgina Angelopoulou <georginangel@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 24, 2023 at 10:45 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with quantifyHAsubregions.sh

        External Email - Use Caution        

Dear Eugenio,

Thank you for your immediate response.

Please see below.

Best,

Georgina

On 24 Jan 2023, at 12:06 PM, Georgina Angelopoulou <georginangel@gmail.com> wrote:

Dear Eugenio,

Thank you for your immediate response.

Please see below.

Best,

Georgina

<Screenshot 2023-01-24 at 12.01.58 PM.png>

On 24 Jan 2023, at 12:27 AM, Georgina Angelopoulou <georginangel@gmail.com> wrote:

Hello Freesurfer experts,

I have accomplished hippocampal subfields segmentation using Freesurfer 7.3.2. However, I have trouble when I try to gather all volumes of all subjects in one single txt file. 

I type quantifyHAsubregions.sh hippoSf T1 testhippo.txt

And the output that appears is:

Gathering results from subjects in: 

   /Users/…/ALBION 

Using the prefix name: 

   hippoSf

Using the suffix name: 

   T1

And writing them to: 

   testhippo.txt 

However, there is no txt file in my directory. I have tried included all subjects’ names in the script and I am still facing the same problem. Do you have any ideas to resolve this?

Thank you in advance,

Best,

Georgina