Re: [Freesurfer] From bedpostX and recon-all to tracula

Hi Kate - The -prep, -bedp, and -path steps need to be run separately, in that order. You can't run them all at once unfortunately. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

a.y

On Wed, 29 Oct 2014, Katherine Damme wrote:

Sorry for the delay. I signed up for the course and hoped that it would answer my question, but I am still unsure what went wrong.

Thank you.

On Tue, Sep 9, 2014 at 12:14 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Can you please attach the trac-all.log file, which has the entire output from beginning to end?
  Ofter something goes wrong earlier that causes the program to fail later in the process.

  Also, we'll need your original configuration file. Thanks!

  On Mon, 8 Sep 2014, Katherine Damme wrote:

        Hello Freesurfer Community!
         
        Thank you Anastasia and Christopher, I am still getting ending with errors and the log
        file gives no clue that I have been able to detect, see attached.

        Any help would be appreciated!


        On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
        wrote:

              Hi Kate - There is an example configuration file for tracula in your
              freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same
              file is also here:
              http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

              If you attach your configuration file and the log file
              (scripts/trac-all.log), we can try to troubleshoot.

              a.y

              On Wed, 3 Sep 2014, Katherine Damme wrote:

              > Hello Freesurfer Community!
              > I have sucessfully completed diffusion preprocessing in FSL and the
              > recon-all of the structural image and would like to use tracula for the
              > tract reconstruction. I keep having trouble with my configuration file.
              >
              > Does anyone have a bedpostX tracula config file they could share as an
              > example?H
              >
              > Thank you!
              >
              > Kate
              >
              >
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