Hi Jenn - I think there was a problem in one of the scripts in the case where CVS registration is used. Can you please try replacing your current version of trac-preproc with the attached version and see if this solves the problem? Please let me know.

Thanks! a.y

On Thu, 10 Oct 2013, Jenn Segawa wrote:

Thanks, Anastasia.  The files are attached.

On Thu, Oct 10, 2013 at 2:37 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  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

        -----------------------------------------------

        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_F
        A.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.n ii. gz--m3z/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/xfms/cvs/final_CV Smorp h_tocvs_avg35.m3z --noDefM3zPath --interp trilin --no-save-reg niiRead(): error openingfile/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.fl t.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


        ---------------------------------------------------------------------
        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
        ---------------------------------------------------------------------
        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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.