External Email - Use Caution
Thanks, Yujing!
Happy new year!
I’m wondering what the first line is in your /usr/local/freesurfer/bin/
asegstats2table
/usr/bin/env python
python asegstats2table –subjects … --tablefile …
python /usr/local/freesurfer/bin/asegstats2table –subjects … --tablefile …
- this worked for me.
Your suggestion worked for me, thanks!
With regards
Vittal
On Mon, Jan 2, 2023 at 3:51 PM Huang, Yujing <yhuan...@mgh.harvard.edu>
wrote:
> Hi Vittal,
>
>
>
> Happy new year!
>
>
>
> I’m wondering what the first line is in your
> /usr/local/freesurfer/bin/asegstats2table. Can you check it by doing ‘head
> /usr/local/freesurfer/bin/asegstats2table’ at the prompt?
>
>
>
> Can you also try the following?
>
> 1. alias python=python2 (as suggested in previous email)
>
> 2. python asegstats2table –subjects … --tablefile …
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* vittal korann <vittalkor...@gmail.com>
> *Sent:* Friday, December 30, 2022 3:56 PM
> *To:* Huang, Yujing <yhuan...@mgh.harvard.edu>
> *Cc:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> * External Email - Use Caution *
>
> Thanks, Yujing, for your quick response.
>
>
>
> I tried your suggestion as well but the same error keeps appearing.
>
>
>
> $ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1
> Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1
> Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1
> Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1
> TOPIRA005_1 TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1
> TOPIRA024_1 TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1
> TOPIRA032_1 Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1
> Tao111_1 Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1
> Tao124_1 Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1
> C008_1 C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1
> C018_1 C019_1 C020_1 C021_1 C023_1 C024_1 --hemi lh --meas. area
> --tablefile Area_aseg_stats txt
>
>
>
> File "/usr/local/freesurfer/bin/asegstats2table", line 195
> print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
> ^
> SyntaxError: invalid syntax
>
>
>
> I do not know where I am going wrong with this.
>
> Any suggestion would be appreciated.
>
>
>
> Thanks,
>
> Vittal
>
>
>
>
>
>
>
> On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing <yhuan...@mgh.harvard.edu>
> wrote:
>
> Hi Vittal,
>
>
>
> I can only repro your error by running ‘python asegstats2table …’. And
> the alias solution works for me.
>
>
>
> Running ‘asegstats2table’ directly doesn’t give me any errors, and it
> doesn’t need the alias setting.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *fsbuild
> *Sent:* Friday, December 30, 2022 12:29 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* vittalkor...@gmail.com
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> * External Email - Use Caution *
>
>
> 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.
>
>
>
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