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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.