Output files are being generated, ie.

  1. dtifit_FA.nii.gz - Fractional Anisotropy
  2. dtifit_MD.nii.gz - Mean Diffusivity
  3. dtifit_MO.nii.gz - Mode of the Anisotropy
  4. dtifit_S0.nii.gz - Non-Diffusion weighted image
  5. dtifit_L1.nii.gz - Primary Eigenvalue
  6. dtifit_L2.nii.gz - Secondary Eigenvalue
  7. dtifit_L3.nii.gz - Tertiary Eigenvalue
  8. dtifit_V1.nii.gz - Primary Eigenvector
  9. dtifit_V2.nii.gz - Secondary Eigenvector
  10. dtifit_V3.nii.gz - Tertiary Eigenvector
But it seems the bedpost process gets cut short and then,  the trac-all path step won't work. I have ran it a few times and the bedpost step ends at the same point. 


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

But do you see the output files from the previous step? The outputs from each step are described on the wiki.


On Sun, 22 May 2016, Jasmin Alves wrote:

Hi Anastasia,
Thank you for the reply, when I do just let it run, I get the following
error when I try to do trac-all -path –c dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin 


On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

      Hi Jasmin - Check if things are running despite that error. Are
      output files being generated?

      a.y

      On Sat, 21 May 2016, Jasmin Alves wrote:


            Dear Freesurfer,

            While doing the bedpost step for TRAC-all ( trac-all
            -bedp -c
            dmrirc1_sim.txt) I received the following error:

            /Applications/freesurfer/bin/bedpostx_mgh: line 345:
            kill: (51042) - No such
            process

            Any ideas?

            Thank you,
            Jasmin 

            Jasmin AlvesPredoctoral Student 
            Medical Biology Graduate Program 
            University of Southern California
            jalves@usc.edu 



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Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jalves@usc.edu 



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--
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Predoctoral Student 
Medical Biology Graduate Program 
University of Southern California