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Thanks, for your quick response.

I installed python2 and did set the default version to python 2.7.18 via aliasing.
But I am getting the same old errors again. The same terminal responses were listed below.
The subjects that are used for aseg/aparc are listed in the folder SUBJECTS under freesurfer

$ asegstats2table --subjects Met001_1 Met002_1 --hemi lh --meas area --tablefile Area_aseg_stats.txt
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?

$which python2
/usr/bin/python2

$ python --version
Python 2.7.18

$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/local/fsl

$ sh aseg_stats_extraction.sh

  File "/usr/local/freesurfer/bin/asegstats2table", line 195
    print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
          ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/asegstats2table", line 195
    print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
          ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?

I also attached the shell script file that I created for thickness and area extraction from the list of subjects.
Is this because something is wrong in the bash_profile/bashrc file? I don't know I am just guessing.

Any help would be appreciated!

Thanks,
Vittal



On Fri, Dec 30, 2022 at 12:29 AM fsbuild <fsbuild@contbay.com> wrote:

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?
It does not look like you are running a python 2.X.  That may be because only python3 is installed by default.

$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...

$ sudo apt update
$ sudo apt install python2

$ which python2
/bin/python2
$ python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you set FREESURFER_HOME and source the freesurfer setup script.  To force “python” to run as “python2” you can try using an alias,

$ alias python=python2
$ python --version
Python 2.7.18

Similarly, if you needed python to run as python3 you could reset the alias to use =python3 instead.

For the error,
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
I would check the subjects you are listing as argument can be found as directories under what SUBJECTS_DIR is currently set to.

- R.