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