Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?
Best,
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti
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Hi Anastasia,
It seems like I do. Could the problem be the config.txt?
Thanks!
Best Regards, Heidi Foo
On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?
a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <heidifoo92@gmail.commailto:heidifoo92@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] trac-all using nifti
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Hi Anastasia,
I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:
: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed
It would be great if you could advise me on what to do.
Thank you!
Best Regards, Heidi Foo
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