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
[cid:image001.png@01D93025.0A5B0240]
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
