You need to specify one more option, like -prep, etc. Please follow the instructions on the tutorial and, if the problem persists, send the exact command line that you ran and the full text of the output that you got.

On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo <heidifoo92@gmail.com> wrote:

        External Email - Use Caution        

Hi Anastasia, 

I think I ran trac-all -c config.txt. 

Regards, 

Heidi 

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

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

---

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

---

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.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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