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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.txtGathering results from subjects in: /usr/local/freesurfer/subjectsUsing the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af S013]# cd ..[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-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/S013Gathering results from subjects in: /usr/local/freesurfer/subjects/S013Using the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af S013]# cd ..[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-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.txtGathering results from subjects in: /usr/local/freesurfer/subjectsUsing the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-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