Hi Jenn - Can you please send the scripts/trac-all.log and your tracula.cfg? I don't have permission to access them.

Thanks, a.y

On Mon, 7 Oct 2013, Jennifer Segawa wrote:

Hello! I'm having problems running the trac-all -tensor step.  dtifit appears to run correctly; the problem seems to be in mapping the output files to the template space.  The command I run is:

trac-all -tensor -c /cluster/manoach/dod/BU_pipeline/data/DOD_DODCON004/tracula.cfg

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And the error I get is (the move file doesn't exist, but dtifit_FA.nii.gz does exist):

mri_vol2vol --mov/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt .nii.gz --targ /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz --o/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii. gz --m3z/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/xfms/cvs/final_CVSmorp h_tocvs_avg35.m3z --noDefM3zPath --interp trilin --no-save-reg niiRead(): error opening file/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt .nii.gz Using the m3z file as it is; no assumed location. movvol/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt .nii.gz targvol /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz outvol/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii. gz invert 0 tal    0 talres 2 regheader 0 noresample 0 interp  trilin (1) precision  float (3) Gdiag_no  -1 Morphing InvertMorph 0 Synth      0 SynthSeed  1381542765 Linux huygens 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Oct  6 12:04:16 EDT 2013

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And here is the output of bugr:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.4 (Final)

Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

machine: huygens

SUBJECTS_DIR: /cluster/manoach/dod/subjects

PWD: /cluster/manoach/dod/BU_pipeline/dti_scripts

ssh huygens   setenv SUBJECTS_DIR /cluster/manoach/dod/subjects   cd /cluster/manoach/dod/BU_pipeline/dti_scripts

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Additionally, the subject is DODCON004 and the script directory can be found at /cluster/manoach/dod/BU_pipeline/data/DODCON004/scripts

Thanks for your help!  Any advice would be appreciated. Jenn Segawa