Hi Elissa,

this is the real error:

SyntaxError: Missing parentheses in call to 'print'

those scripts use the Python 2 print command and you are running them with Python 3.

In 3, print needs to be like
print("Hello world!")
in 2 it was simply
print "Hello world!"

so make sure you run them with Python 2.

Best, Martin

On 11/13/2015 03:04 PM, Elissa Ash wrote:

Dear Freesurfer support,

I am very new to freesurfer and I thank you in advance for your assistance. I have been trying to run the group analysis tutorial (qdec) and I have encountered the following error messages. I was unable to generate the stats data tables in the tutorial and received the following types of error messages:

1) When trying to run asestats2table in qdec I get an error message that says that the subjects are not specified although they are. The $SUBJECTS_DIR is correct. I even encounter the same error when I just try to run asegstats2table --help (see below):

tegmentum:group_analysis_tutorial gazzlab16$ asegstats2table --subjects 004 045 091 --meas volume --tablefile aseg_stats.txt

  File "/Applications/freesurfer/bin/asegstats2table", line 186

    print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'

                                                                      ^

SyntaxError: invalid syntax

tegmentum:freesurfer gazzlab16$ asegstats2table --help

  File "/Applications/freesurfer/bin/asegstats2table", line 186

    print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'

                                                                      ^

SyntaxError: invalid syntax

2) When trying to run asestats2table I get an error message that says that at least one subject must be provided although they are. The $SUBJECTS_DIR is correct. I even encounter the same error when I just try to run aparcstats2table --help (see below):

tegmentum:group_analysis_tutorial gazzlab16$ aparcstats2table --subjects 004 045 091 --hemi rh --meas thickness --tablefile aparc_stats.txt

  File "/Applications/freesurfer/bin/aparcstats2table", line 151

    print 'ERROR: atleast 1 subject must be provided'

                                                    ^

SyntaxError: Missing parentheses in call to 'print'

tegmentum:group_analysis_tutorial gazzlab16$ aparcstats2table --help

  File "/Applications/freesurfer/bin/aparcstats2table", line 151

    print 'ERROR: atleast 1 subject must be provided'

                                                    ^

SyntaxError: Missing parentheses in call to 'print'

I am not sure how to proceed. Thank you again for your assistance.

Sincerely,

Elissa

-- 

Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology

Tel Aviv Sourasky Medical Center

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu 

_______________________________________________
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 Partners Compliance HelpLine at
http://www.partners.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.