[root@localhost 140518MS]# trac-all -prep -c dmrirc
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
INFO: Diffusion root is /usr/local/freesurfer/subjects/
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /usr/local/freesurfer/subjects//140518MS/scripts/dmrirc.local -log /usr/local/freesurfer/subjects//140518MS/scripts/trac-all.log -cmd /usr/local/freesurfer/subjects//140518MS/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Sun Jun 29 18:41:21 PDT 2014
mri_convert /usr/local/freesurfer/subjects/140518MS/diffusion/i0000001.dcm /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.nii.gz
mri_convert /usr/local/freesurfer/subjects/140518MS/diffusion/i0000001.dcm /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/140518MS/diffusion/i0000001.dcm...
Starting DICOMRead2()
dcmfile = /usr/local/freesurfer/subjects/140518MS/diffusion/i0000001.dcm
dcmdir = /usr/local/freesurfer/subjects/140518MS/diffusion
Ref Series No = 6
Found 3254 files, checking for dicoms
Found 3250 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2.39998
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 65
nslices = 50
ndcmfiles = 3250
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=15000.00, TE=72.60, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.nii.gz...
mri_probedicom --i /usr/local/freesurfer/subjects/140518MS/diffusion/i0000001.dcm > /usr/local/freesurfer/subjects//140518MS/dmri/dcminfo.dat
cp /usr/local/freesurfer/subjects/140518MS/diffusion/bvecs.txt /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvecs
cp /usr/local/freesurfer/subjects/140518MS/diffusion/bvals.txt /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvals
mv -f /usr/local/freesurfer/subjects//140518MS/dmri/bvecs.tmp /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvecs
mv -f /usr/local/freesurfer/subjects//140518MS/dmri/bvals.tmp /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvals
flip4fsl /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.nii.gz /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 13.824
fslswapdim /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.nii.gz x -y z /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.nii.gz
INFO: found /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.mghdti.bvecs /usr/local/freesurfer/subjects//140518MS/dmri/bvecs
mv -f /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.mghdti.bvals /usr/local/freesurfer/subjects//140518MS/dmri/bvals
eddy_correct /usr/local/freesurfer/subjects//140518MS/dmri/dwi_orig_flip.nii.gz /usr/local/freesurfer/subjects//140518MS/dmri/dwi.nii.gz 0
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0000
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0001
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0002
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0003
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0004
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0005
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0006
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0007
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0008
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0009
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0010
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0011
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0012
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0013
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0014
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0015
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0016
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0017
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0018
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0019
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0020
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0021
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0022
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0023
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0024
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0025
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0026
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0027
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0028
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0029
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0030
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0031
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0032
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0033
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0034
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0035
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0036
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0037
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0038
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0039
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0040
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0041
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0042
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0043
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0044
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0045
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0046
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0047
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0048
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0049
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0050
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0051
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0052
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0053
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0054
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0055
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0056
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0057
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0058
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0059
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0060
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0061
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0062
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0063
processing /usr/local/freesurfer/subjects//140518MS/dmri/dwi_tmp0064
mv -f /usr/local/freesurfer/subjects//140518MS/dmri/bvecs /usr/local/freesurfer/subjects//140518MS/dmri/bvecs.norot
xfmrot /usr/local/freesurfer/subjects//140518MS/dmri/dwi.ecclog /usr/local/freesurfer/subjects//140518MS/dmri/bvecs.norot /usr/local/freesurfer/subjects//140518MS/dmri/bvecs
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
ln -sf /usr/local/freesurfer/subjects//140518MS/dmri/dwi.nii.gz /usr/local/freesurfer/subjects//140518MS/dmri/data.nii.gz
mri_convert --frame 65 /usr/local/freesurfer/subjects//140518MS/dmri/dwi.nii.gz /usr/local/freesurfer/subjects//140518MS/dmri/dwi_frame65.nii.gz
mri_convert --frame 65 /usr/local/freesurfer/subjects//140518MS/dmri/dwi.nii.gz /usr/local/freesurfer/subjects//140518MS/dmri/dwi_frame65.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects//140518MS/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 65
ERROR: fMRIframe: frame >= nframes
Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Jun 29 18:43:46 PDT 2014