It looks to me like there was an error at an earlier stage, in the -prior step, so some of the files that the -path step is looking for are not correct. Look for "img2imgcoord: Command not found." That's a command from FSL that it can't find. (The 5.2 version of trac-all will not use this any more, BTW.)

On Mon, 25 Feb 2013, Susan Kuo wrote:

Yes - I'm attaching the trac-all.log. The failure occurred right above this line:  'trac-paths finished without error at Mon Feb 25 14:08:44 EST 2013'

if you want to search through the text.

The terminal actually showed 2 errors (only the second is recorded in trac-all.log:

1 - 'Segmentation fault (core dumped)' ---mentioned previously and  2 - 'ERROR: must specify input volume(s)' -- which I receive after the program tries to run the below command,

---

/usr/local/freesurfer/bin/dmri_mergepaths --indir/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa th --in --out/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa th/merged_avg33_mni_flt.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s)

---

I'm currently re-running priors and using 32 training subjects plus the subject's data. Any insight you can offer would be appreciated.

Thank you for your help! Susie  On Mon, Feb 25, 2013 at 3:47 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Susan - Can you please send your entire trac-all.log? I'll
  need to see what else was going on before the error message
  occurred.

  Thanks,
  a.y

  On Mon, 25 Feb 2013, Susan Kuo wrote:

        Hi FreeSurfer Community,    I am trying to run
        TRACULA's last step,
        'trac-all -path -c <path-to-dmrirc-config-script>',
        and am receiving the
        error: 

        Segmentation fault(core dumped)

        Moreover, when I look to standard output (terminal),
        I noticed that the
        initial 'dmri_paths' command is incomplete. The
        terminal shows that the
        command includes the '--init' switch and several
        arguments (e.g. '<subject
        ID>/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'),
        the last of which is
        terminated mid-pathname. Can anyone suggest a reason
        why this would be the
        case? 




        Thank you, 
        Susie Kuo

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