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
External Email - Use Caution 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