Hello again,

Thank you for sending the screenshot and additional information.

It looks like your directory structure is correct. It also looks like you are correct about the python version causing your error.

That utility is written in Python 2.7, and it appears that your environment is sourcing some version of Python 3. (You can confirm this by running the command 'python --version' in your terminal).

You need to check that you have a version of Python2.7 installed, and then add that to your path.

To check that you have a version of Python2.7: run the command 'which python2'. If a version of Python2.7 is installed, the path to it will be printed in the terminal. If no version of is found, you will need to install one.

To source that python version (add it to your path): run 'export PATH="</path/to/python2.7/>":$PATH'

Best,

Jackson


From: Zeynep Boz <zeynep.boz@omu.edu.tr>
Sent: Friday, June 4, 2021 2:00 PM
To: Nolan, Jackson <JNOLAN5@mgh.harvard.edu>
Subject: Re: 'help: aparcstats2table'
 

        External Email - Use Caution        

Dear Jackson,

I run these commands "FreesurferWork on my computer" in the directory containing that subject. My subject is H1_deneme in named directory FreesurferWork 
According to the comments I read, I think this error may be related to the phyton version, but of course you know better.
Attached I am sending you a screenshot of the terminal and the folders with the file directories.

Thank you for your support
I wish you good work


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

Kimden: "Nolan, Jackson" <JNOLAN5@mgh.harvard.edu>
Kime: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>, "zeynep boz" <zeynep.boz@omu.edu.tr>
Gönderilenler: 2 Haziran Çarşamba 2021 23:20:11
Konu: Re: 'help: aparcstats2table'

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'
 

        External Email - Use Caution        

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

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