What is the trac-all command line that you run?

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <heidifoo92@gmail.com>
Sent: Wednesday, September 19, 2018 11:06:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti

 

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Hi Anastasia,

Nope, I don't actually get any output and/or log file. 

Regards, 

Heidi Foo 

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

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

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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

 

        External Email - Use Caution        

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.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.edu> on behalf of Heidi Emmanuel Foo <heidifoo92@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, September 17, 2018 at 12:55 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] trac-all using nifti

        External Email - Use Caution        

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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