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I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue.
Many thanks in advance. Regards Devika K Research Scholar, Dept of EEE e: k_devika@cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India
Hi Devika
In the future can you include the text of the command and the output in your email instead of a screenshot? That will make our job easier.
Try specifying which subjects you want processed explicitly with --subjects
cheers Bruce
On Sun, 19 Jan 2020, Devika K wrote:
External Email - Use Caution
I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue.
Many thanks in advance.[cleardot.gif] Regards Devika K Research Scholar, Dept of EEE e: k_devika@cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India
Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must be run with python2. Your error implies that the python in your PATH points to python3. You should make sure python points to a python2 version before running freesurfer. Sorry for the inconvenience. Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Devika K devikakuttala@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Sunday, January 19, 2020 at 9:09 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table error
External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue.
Many thanks in advance. [Image removed by sender.] Regards Devika K Research Scholar, Dept of EEE e: k_devika@cb.students.amrita.edumailto:k_devika@cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India
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Hi Devika, I ran into the same issue and in case you don’t want to change your PATH (like me), another option is to edit aparcstats2table script and simply replace the shebang from “#!/usr/bin/env python” to e.g. “#!/usr/bin/env python2” (please make sure “which python2” returns something in a terminal). Cheers Antonin
On 19 Jan 2020, at 20:35, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote:
Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must be run with python2. Your error implies that the python in your PATH points to python3. You should make sure python points to a python2 version before running freesurfer. Sorry for the inconvenience. Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Devika K <devikakuttala@gmail.commailto:devikakuttala@gmail.com> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, January 19, 2020 at 9:09 AM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] aparcstats2table error
External Email - Use Caution
I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue.
Many thanks in advance. [Image removed by sender.] Regards Devika K Research Scholar, Dept of EEE e: k_devika@cb.students.amrita.edumailto:k_devika@cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India
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