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
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
External Email - Use Caution
Dear Eugenio,
Thank you for your immediate response.
Please see below.
Best, Georgina

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
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
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
freesurfer@nmr.mgh.harvard.edu
-
Georgina Angelopoulou -
Iglesias Gonzalez, Juan E.