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....@omu.edu.tr>
Sent: Friday, June 4, 2021 2:00 PM
To: Nolan, Jackson <jnol...@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" <jnol...@mgh.harvard.edu>
Kime: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>, "zeynep boz"
<zeynep....@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeynep Boz
<zeynep....@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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
