Dear Georgina,

Can you please send me the list of files (a screenshot is also fine) inside the mri directory of any of your subjects, please?

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: Monday, January 23, 2023 at 17:28
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Problem with quantifyHAsubregions.sh

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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