Dear Developer and Eugenio,

Thank you for the suggestion! I tried to cd into FreeSurfer root or the specific folder which contains the data (i.e., /usr/local/freesurfer/subjects/S013 or /usr/local/freesurfer/subjects), and also tried to make the optional argument to override the subjects directory (i.e., /usr/local/freesurfer/subjects/S013 or /usr/local/freesurfer/subjects)

However, even doing so, there's still no .txt file to be written since couldn't find it in any of the folders. ( we applied the 'find' command, too) Could you way in any more suggestions? Thank you in advance!

Here're the terminal commands:

[root@d7d0454589af S013]# quantifyHAsubregions.sh hippoSf T1 results013.txt
Gathering results from subjects in:
   /usr/local/freesurfer/subjects
Using the prefix name:
   hippoSf
Using the suffix name:
   T1
And writing them to:
   results013.txt
[root@d7d0454589af S013]# cd ..
[root@d7d0454589af subjects]# ls -l
total 12316
-rw-rw-r--  1 root root    1512 Jul 23  2020 README
drwx--S--- 11 root root    4096 Jun  7 06:32 S013
drwxrwsr-x  6 root root    4096 Nov 11  2008 V1_average
drwxrwsr-x 10 root root    4096 Jul 23  2020 bert
drwxrwsr-x 12 root root    4096 Mar 13  2012 cvs_avg35
drwxrwsr-x 13 root root    4096 Apr 14  2015 cvs_avg35_inMNI152
drwxrwsr-x  8 root root    4096 Nov 13  2015 fsaverage
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage3
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage4
drwxrwsr-x  8 root root    4096 May 31  2011 fsaverage5
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage6
drwxrwsr-x 12 root root    4096 Aug 20  2012 fsaverage_sym
drwxrwsr-x  6 root root    4096 Mar 30  2010 lh.EC_average
drwxrwsr-x  6 root root    4096 Mar 30  2010 rh.EC_average
-rw-rw-r--  1 root root 6280209 Jul 23  2020 sample-001.mgz
-rw-rw-r--  1 root root 6269785 Jul 23  2020 sample-002.mgz
[root@d7d0454589af subjects]# cd S013
[root@d7d0454589af S013]# quantifyHAsubregions.sh hippoSf T1 results013.txt /usr/local/freesurfer/subjects/S013
Gathering results from subjects in:
   /usr/local/freesurfer/subjects/S013
Using the prefix name:
   hippoSf
Using the suffix name:
   T1
And writing them to:
   results013.txt
[root@d7d0454589af S013]# cd ..
[root@d7d0454589af subjects]# ls -l
total 12316
-rw-rw-r--  1 root root    1512 Jul 23  2020 README
drwx--S--- 11 root root    4096 Jun  7 06:32 S013
drwxrwsr-x  6 root root    4096 Nov 11  2008 V1_average
drwxrwsr-x 10 root root    4096 Jul 23  2020 bert
drwxrwsr-x 12 root root    4096 Mar 13  2012 cvs_avg35
drwxrwsr-x 13 root root    4096 Apr 14  2015 cvs_avg35_inMNI152
drwxrwsr-x  8 root root    4096 Nov 13  2015 fsaverage
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage3
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage4
drwxrwsr-x  8 root root    4096 May 31  2011 fsaverage5
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage6
drwxrwsr-x 12 root root    4096 Aug 20  2012 fsaverage_sym
drwxrwsr-x  6 root root    4096 Mar 30  2010 lh.EC_average
drwxrwsr-x  6 root root    4096 Mar 30  2010 rh.EC_average
-rw-rw-r--  1 root root 6280209 Jul 23  2020 sample-001.mgz
-rw-rw-r--  1 root root 6269785 Jul 23  2020 sample-002.mgz
[root@d7d0454589af subjects]# quantifyHAsubregions.sh hippoSf T1 results013.txt
Gathering results from subjects in:
   /usr/local/freesurfer/subjects
Using the prefix name:
   hippoSf
Using the suffix name:
   T1
And writing them to:
   results013.txt
[root@d7d0454589af subjects]# ls -l
total 12316
-rw-rw-r--  1 root root    1512 Jul 23  2020 README
drwx--S--- 11 root root    4096 Jun  7 06:32 S013
drwxrwsr-x  6 root root    4096 Nov 11  2008 V1_average
drwxrwsr-x 10 root root    4096 Jul 23  2020 bert
drwxrwsr-x 12 root root    4096 Mar 13  2012 cvs_avg35
drwxrwsr-x 13 root root    4096 Apr 14  2015 cvs_avg35_inMNI152
drwxrwsr-x  8 root root    4096 Nov 13  2015 fsaverage
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage3
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage4
drwxrwsr-x  8 root root    4096 May 31  2011 fsaverage5
drwxrwsr-x  8 root root    4096 Sep 22  2009 fsaverage6
drwxrwsr-x 12 root root    4096 Aug 20  2012 fsaverage_sym
drwxrwsr-x  6 root root    4096 Mar 30  2010 lh.EC_average
drwxrwsr-x  6 root root    4096 Mar 30  2010 rh.EC_average
-rw-rw-r--  1 root root 6280209 Jul 23  2020 sample-001.mgz
-rw-rw-r--  1 root root 6269785 Jul 23  2020 sample-002.mgz

Best regards,

Josephine