[server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config
INFO: SUBJECTS_DIR is /MRI/Tracula-test
INFO: Diffusion root is /MRI/Tracula-test
Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /Applications/Freesurfer5.3/freesurfer
    Previous: /Volumes/Data/Freesurfer_5.3/freesurfer
trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd
#-------------------------------------
/Applications/Freesurfer5.3/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed Jul  2 23:46:32 BRT 2014
mri_convert /MRI/Tracula-test///1492/1.3.12.2.1107.5.2.31.30747.2012061308004412260204165.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz
mri_convert /MRI/Tracula-test///1492/1.3.12.2.1107.5.2.31.30747.2012061308004412260204165.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /MRI/Tracula-test///1492/1.3.12.2.1107.5.2.31.30747.2012061308004412260204165.dcm...
Getting Series No 
INFO: Found 6602 files in /MRI/Tracula-test///1492
INFO: Scanning for Series Number 3
Scanning Directory 
INFO: found 6500 files in series
INFO: loading series header info.

RunNo = 2
INFO: sorting.
INFO: (120 120  50), nframes = 130, ismosaic=0
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 		/MRI/Tracula-test///1492/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280.dcm
Identification
	NumarisVer        syngo MR B15
	ScannerModel      Espree
	PatientName       MACHADO^ANA M P 
Date and time
	StudyDate         20120613
	StudyTime         074845.171000 
	SeriesTime        080047.531000 
	AcqTime           080046.267500 
Acquisition parameters
	PulseSeq          *ep_b0
	Protocol          DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          110
	InversionTime     -1
	RepetitionTime    8000
	PhEncFOV          240
	ReadoutFOV        240
Image information
	RunNo             2
	SeriesNo          3
	ImageNo           1
	NImageRows        120
	NImageCols        120
	NFrames           130
	SliceArraylSize   50
	IsMosaic          0
	ImgPos            116.6747  79.4248 -34.6722 
	VolRes              2.0000   2.0000   2.7000 
	VolDim            120      120       50 
	Vc                 -1.0000  -0.0000   0.0000 
	Vr                 -0.0000  -1.0000  -0.0052 
	Vs                 -0.0000  -0.0052   1.0000 
	VolCenter          -3.3253 -40.9270  32.1985 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!). 
TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -0.999986, -0.00523596)
k_ras = (-0, -0.00523596, 0.999986)
writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz...
mri_probedicom --i /MRI/Tracula-test///1492/1.3.12.2.1107.5.2.31.30747.2012061308004412260204165.dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat
cp /MRI/Tracula-test//bvec65.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs
cp /MRI/Tracula-test//bval65.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals
mv -f /MRI/Tracula-test/ESNA149/dmri/bvecs.tmp /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs
mv -f /MRI/Tracula-test/ESNA149/dmri/bvals.tmp /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals
flip4fsl /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10.8
fslswapdim /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz x -y z /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.nii.gz
INFO: found /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.mghdti.bvecs /MRI/Tracula-test/ESNA149/dmri/bvecs
mv -f /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.mghdti.bvals /MRI/Tracula-test/ESNA149/dmri/bvals
mv -f /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.nii.gz /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz
ln -sf /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz /MRI/Tracula-test/ESNA149/dmri/data.nii.gz
mri_convert --frame 0 /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz /MRI/Tracula-test/ESNA149/dmri/dwi_frame0.nii.gz
mri_convert --frame 0 /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz /MRI/Tracula-test/ESNA149/dmri/dwi_frame0.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz...
TR=8000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.999986, 0.00523596)
k_ras = (0, -0.00523596, 0.999986)
keeping frame 0
writing to /MRI/Tracula-test/ESNA149/dmri/dwi_frame0.nii.gz...
mri_concat --i /MRI/Tracula-test/ESNA149/dmri/dwi_frame0.nii.gz --mean --o /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Computing mean across frames
Writing to /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz
bet /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz /MRI/Tracula-test/ESNA149/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /MRI/Tracula-test/ESNA149/dmri/lowb_brain_mask.nii.gz /MRI/Tracula-test/ESNA149/dlabel/diff
#-------------------------------------
#@# Image quality assessment Wed Jul  2 23:56:35 BRT 2014
/Applications/Freesurfer5.3/freesurfer/bin/dmri_motion --dwi /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz --mat /MRI/Tracula-test/ESNA149/dmri/dwi.ecclog --bval /MRI/Tracula-test/ESNA149/dmri/bvals --out /MRI/Tracula-test/ESNA149/dmri/dwi_motion.txt

cwd /MRI/Tracula-test
cmdline /Applications/Freesurfer5.3/freesurfer/bin/dmri_motion --dwi /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz --mat /MRI/Tracula-test/ESNA149/dmri/dwi.ecclog --bval /MRI/Tracula-test/ESNA149/dmri/bvals --out /MRI/Tracula-test/ESNA149/dmri/dwi_motion.txt 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa
Output motion measure file: /MRI/Tracula-test/ESNA149/dmri/dwi_motion.txt
Input transform file: /MRI/Tracula-test/ESNA149/dmri/dwi.ecclog
Input DWI file: /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz
Input b-value table: /MRI/Tracula-test/ESNA149/dmri/bvals
Low-b image intensity threshold: 100
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
ERROR: Could not open /MRI/Tracula-test/ESNA149/dmri/dwi.ecclog for reading
Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Wed Jul  2 23:56:35 BRT 2014