bash-3.2$ trac-all -prep -c config_file
set: Syntax Error.
INFO: SUBJECTS_DIR is /Users/alca/Applications/freesurfer/subjects
INFO: Diffusion root is /Users/alca/Applications/freesurfer/subjects
Actual FREESURFER_HOME /Users/alca/Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /Users/alca/Applications/freesurfer
    Previous: /soft/freesurfer/5.3.0
trac-preproc -c /Users/alca/Applications/freesurfer/subjects/c002/scripts/dmrirc.local -log /Users/alca/Applications/freesurfer/subjects/c002/scripts/trac-all.log -cmd /Users/alca/Applications/freesurfer/subjects/c002/scripts/trac-all.cmd
#-------------------------------------
/Users/alca/Applications/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Mon Oct 13 11:30:22 CDT 2014
mri_convert /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig.nii.gz
mri_convert /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm...
Getting Series No 
INFO: Found 42 files in /Users/alca/DTI_MPS/c002/DTI
INFO: Scanning for Series Number 9
Scanning Directory 
INFO: found 39 files in series
INFO: loading series header info.

RunNo = 8
WARNING: Run 1 appears to be truncated
  Files Found: 39, Files Expected (lRep+1): 3
FileName                /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm
Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim 
        PatientName       002-1 
Date and time
        StudyDate         20121013
        StudyTime         083722.062000 
        SeriesTime        090553.546000 
        AcqTime           090520.980000 
Acquisition parameters
        PulseSeq          *ep_b0
        Protocol          ep2d_diff_12dir 
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          90
        InversionTime     -1
        RepetitionTime    8500
        PhEncFOV          256
        ReadoutFOV        256
Image information
        RunNo             8
        SeriesNo          9
        ImageNo           1
        NImageRows        1024
        NImageCols        1024
        NFrames           39
        SliceArraylSize   64
        IsMosaic          1
        ImgPos            1026.1693 1024.3661 -43.1366 
        VolRes              2.0000   2.0000   2.0000 
        VolDim            128      128       64 
        Vc                 -1.0000  -0.0000   0.0000 
        Vr                 -0.0000  -1.0000   0.0000 
        Vs                 -0.0000  -0.0000   1.0000 
        VolCenter           0.0000   0.0000   0.0000 
        TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128  64), nframes = 39, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 8500, TR = 8500 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
FileName                /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm
Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim 
        PatientName       002-1 
Date and time
        StudyDate         20121013
        StudyTime         083722.062000 
        SeriesTime        090553.546000 
        AcqTime           090520.980000 
Acquisition parameters
        PulseSeq          *ep_b0
        Protocol          ep2d_diff_12dir 
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          90
        InversionTime     -1
        RepetitionTime    8500
        PhEncFOV          256
        ReadoutFOV        256
Image information
        RunNo             8
        SeriesNo          9
        ImageNo           1
        NImageRows        1024
        NImageCols        1024
        NFrames           39
        SliceArraylSize   64
        IsMosaic          1
        ImgPos            130.1693 128.3661 -43.1366 
        VolRes              2.0000   2.0000   2.0000 
        VolDim            128      128       64 
        Vc                 -1.0000  -0.0000   0.0000 
        Vr                 -0.0000  -1.0000   0.0000 
        Vs                 -0.0000  -0.0000   1.0000 
        VolCenter           2.1693   0.3661  20.8634 
        TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!). 
TR=8500.00, TE=90.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Users/alca/DTI_MPS/c002/DTI/MR-ST001-SE009-0001.dcm > /Users/alca/Applications/freesurfer/subjects/c002/dmri/dcminfo.dat
flip4fsl /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig.nii.gz /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig.nii.gz
 x -y z /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig_flip.nii.gz
mv -f /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig_flip.mghdti.bvecs /Users/alca/Applications/freesurfer/subjects/c002/dmri/bvecs
mv: rename /Users/alca/Applications/freesurfer/subjects/c002/dmri/dwi_orig_flip.mghdti.bvecs to /Users/alca/Applications/freesurfer/subjects/c002/dmri/bvecs: No such file or directory
Darwin alenas-mbp.pk5001z 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Oct 13 11:31:26 CDT 2014