Hello Dr. Zeynep,

Are you running those commands in the directory containing that subject? The script needs the file path to the subject, and absolute paths tend to work better than relative paths.

If you have specified these are still getting those errors, please send your full terminal output with the command run and all error messages.

Best,
Jackson
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeynep Boz <zeynep.boz@omu.edu.tr>
Sent: Saturday, May 29, 2021 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] 'help: aparcstats2table'
 

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Hello,
I am using Ubuntu 18.05 version and Freesurfer6 version.
I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part.
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness --tablefile lh.thicknes.xlsx" gives the following error:
   File "/usr/local/freesurfer/bin/aparcstats2table", line 156
     print 'ERROR: atleast 1 subject must be provided'
   On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas volume --stats = aseg.stats --table = segstats.txt" gives the following error:
   File "/usr/local/freesurfer/bin/asegstats2table", line 195
     print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Thank you in advance for your support



Dr.Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261