[server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning
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 -no-isrunning
#-------------------------------------
/Applications/Freesurfer5.3/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Thu Jul  3 13:26:17 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//bval.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
eddy_correct /MRI/Tracula-test/ESNA149/dmri/dwi_orig_flip.nii.gz /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz 0
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0000
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0001
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0002
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0003
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0004
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0005
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0006
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0007
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0008
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0009
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0010
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0011
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0012
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0013
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0014
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0015
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0016
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0017
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0018
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0019
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0020
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0021
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0022
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0023
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0024
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0025
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0026
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0027
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0028
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0029
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0030
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0031
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0032
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0033
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0034
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0035
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0036
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0037
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0038
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0039
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0040
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0041
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0042
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0043
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0044
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0045
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0046
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0047
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0048
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0049
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0050
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0051
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0052
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0053
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0054
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0055
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0056
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0057
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0058
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0059
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0060
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0061
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0062
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0063
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0064
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0065
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0066
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0067
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0068
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0069
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0070
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0071
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0072
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0073
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0074
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0075
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0076
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0077
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0078
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0079
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0080
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0081
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0082
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0083
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0084
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0085
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0086
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0087
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0088
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0089
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0090
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0091
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0092
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0093
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0094
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0095
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0096
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0097
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0098
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0099
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0100
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0101
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0102
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0103
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0104
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0105
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0106
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0107
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0108
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0109
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0110
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0111
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0112
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0113
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0114
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0115
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0116
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0117
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0118
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0119
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0120
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0121
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0122
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0123
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0124
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0125
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0126
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0127
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0128
processing /MRI/Tracula-test/ESNA149/dmri/dwi_tmp0129
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=1000.00, 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 Thu Jul  3 14:18:58 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
Computing between-volume head motion measures
INFO: Processed transforms for 130 volumes
Loading DWI volume series from /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz
Loading b-value table from /MRI/Tracula-test/ESNA149/dmri/bvals
Computing within-volume head motion measures
Done in 11.097 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Thu Jul  3 14:19:10 BRT 2014
mri_convert /MRI/Tracula-test/ESNA149/mri/brain.mgz /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz
mri_convert /MRI/Tracula-test/ESNA149/mri/brain.mgz /MRI/Tracula-test/ESNA149/dmri/brain_anat_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/ESNA149/mri/brain.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.31718e-08, -1.05853e-07)
j_ras = (1.05853e-07, 2.32832e-10, -1)
k_ras = (1.59497e-07, 1, -3.49248e-10)
writing to /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz...
flip4fsl /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz x z -y /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz
tkregister2 --mov /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz --targ /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2anat.mat --reg /MRI/Tracula-test/ESNA149/dmri/xfms/anat2anatorig.dat
tkregister_tcl /Applications/Freesurfer5.3/freesurfer/tktools/tkregister2.tcl
target  volume /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz
movable volume /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz
reg file       /MRI/Tracula-test/ESNA149/dmri/xfms/anat2anatorig.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.000  -0.000   0.000   0.000;
-0.000   1.000   0.000   0.000;
-0.000   0.000   1.000   1.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000  -0.000   0.000   0.000;
-0.000   1.000   0.000   0.000;
-0.000   0.000   1.000   1.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
 1.000   0.000  -0.000   0.000;
-0.000  -0.000  -1.000  -0.000;
 0.000   1.000   0.000   1.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2anatorig.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2anat.mat
flirt -in /MRI/Tracula-test/ESNA149/dmri/lowb_brain.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz -out /MRI/Tracula-test/ESNA149/dmri/lowb_brain_anat.flt.nii.gz -omat /MRI/Tracula-test/ESNA149/dmri/xfms/diff2anat.flt.mat -cost corratio
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/diff2anat.flt.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2diff.flt.mat -concat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/diff2anatorig.flt.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2diff.flt.mat
#-------------------------------------
#@# Inter-subject registration Thu Jul  3 14:20:08 BRT 2014
flirt -in /MRI/Tracula-test/ESNA149/dmri/brain_anat.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dmri/brain_anat_mni.nii.gz -omat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/mni2anat.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/diff2mni.flt.mat -concat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat /MRI/Tracula-test/ESNA149/dmri/xfms/diff2anat.flt.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/mni2diff.flt.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/diff2mni.flt.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2mni.mat -concat /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /MRI/Tracula-test/ESNA149/dmri/xfms/mni2anatorig.mat -inverse /MRI/Tracula-test/ESNA149/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Thu Jul  3 14:23:16 BRT 2014
mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter.nii.gz
Binarizing based on matching values
nMatch 5
 0     2
 1     7
 2    41
 3    46
 4    77
binval        1
binvalnot     0
Found 607197 values in range
Counting number of voxels
Found 607197 voxels in final mask
mri_binarize done
mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter++.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter++.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter++.nii.gz
Binarizing based on matching values
nMatch 8
 0     2
 1     7
 2    41
 3    46
 4    77
 5    28
 6    60
 7    16
binval        1
binvalnot     0
Found 626749 values in range
Counting number of voxels
Found 626749 voxels in final mask
mri_binarize done
mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
 0     4
 1    43
binval        0
binvalnot     1
Found 10556 values in range
Counting number of voxels
Found 10556 voxels in final mask
mri_binarize done
mri_aparc2aseg --s ESNA149 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /MRI/Tracula-test
subject ESNA149
outvol /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 2.000000
RipUnknown 0

Reading lh white surface 
 /MRI/Tracula-test/ESNA149/surf/lh.white

Reading lh pial surface 
 /MRI/Tracula-test/ESNA149/surf/lh.pial

Loading lh annotations from /MRI/Tracula-test/ESNA149/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /MRI/Tracula-test/ESNA149/surf/rh.white

Reading rh pial surface 
 /MRI/Tracula-test/ESNA149/surf/rh.pial

Loading rh annotations from /MRI/Tracula-test/ESNA149/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /MRI/Tracula-test/ESNA149/mri/ribbon.mgz
Loading filled from /MRI/Tracula-test/ESNA149/mri/filled.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /MRI/Tracula-test/ESNA149/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1058864
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 2 clusters
     0 k 2.000000
     1 k 4167.000000
Fixing Parahip RH WM
  Found 6 clusters
     0 k 15.000000
     1 k 2.000000
     2 k 1.000000
     3 k 1.000000
     4 k 3.000000
     5 k 1919.000000
Writing output aseg to /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min        1000
max        2999
binval        1
binvalnot     0
Found 483819 values in range
Counting number of voxels
Found 483819 voxels in final mask
mri_binarize done
mri_binarize --i /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min        1000
max        4999
binval        1
binvalnot     0
Found 808260 values in range
Counting number of voxels
Found 808260 voxels in final mask
mri_binarize done
mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 16 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/Brain-Stem.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /MRI/Tracula-test
cmdline mri_binarize --i /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz --match 16 --o /MRI/Tracula-test/ESNA149/dlabel/anatorig/Brain-Stem.nii.gz 
sysname  Darwin
hostname server.macbookpro.com
machine  x86_64
user     pedrogomesrosa

input      /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /MRI/Tracula-test/ESNA149/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
 0    16
binval        1
binvalnot     0
Found 12705 values in range
Counting number of voxels
Found 12705 voxels in final mask
mri_binarize done
fslmaths /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz -add /MRI/Tracula-test/ESNA149/dlabel/anatorig/Brain-Stem.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /MRI/Tracula-test/ESNA149/mri/brainmask.mgz /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert /MRI/Tracula-test/ESNA149/mri/brainmask.mgz /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.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/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.31718e-08, -1.05853e-07)
j_ras = (1.05853e-07, 2.32832e-10, -1)
k_ras = (1.59497e-07, 1, -3.49248e-10)
writing to /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.nii.gz -mul /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert /MRI/Tracula-test/ESNA149/mri/aparc+aseg.mgz /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.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/mri/aparc+aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.31718e-08, -1.05853e-07)
j_ras = (1.05853e-07, 2.32832e-10, -1)
k_ras = (1.59497e-07, 1, -3.49248e-10)
writing to /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg_mask.nii.gz
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/White-Matter.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/White-Matter.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter++.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/White-Matter++.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter++.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter++.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter++.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/White-Matter++.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/White-Matter++.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/notventricles.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/notventricles.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/notventricles.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/notventricles.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/notventricles.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/notventricles.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/notventricles.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/cortex.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/cortex.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/cortex.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/cortex.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/cortex+2mm.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm+bs.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm+bs.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm+bs.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm+bs.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/cortex+2mm+bs.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/cortex+2mm+bs.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/aparc+aseg.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg+2mm.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg+2mm.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/aparc+aseg+2mm.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg_mask.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg_mask.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg_mask.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg_mask.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/aparc+aseg_mask.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/aparc+aseg_mask.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/anat_brain_mask.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask-vent.nii.gz /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /MRI/Tracula-test/ESNA149/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask-vent.nii.gz
fslorient -forceradiological /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask-vent.nii.gz
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/lowb.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/diff/anat_brain_mask-vent.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz -k /MRI/Tracula-test/ESNA149/dlabel/diff/White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}' > /MRI/Tracula-test/ESNA149/dmri/dwi_snr.txt
flirt -in /MRI/Tracula-test/ESNA149/dlabel/diff/lowb_brain_mask.nii.gz -ref /Applications/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour
flirt -in /MRI/Tracula-test/ESNA149/dlabel/diff/lowb_brain_mask.nii.gz -ref /MRI/Tracula-test/ESNA149/dmri/brain_anat_orig.nii.gz -out /MRI/Tracula-test/ESNA149/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /MRI/Tracula-test/ESNA149/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour
ln -sf /MRI/Tracula-test/ESNA149/dlabel/diff/lowb_brain_mask.nii.gz /MRI/Tracula-test/ESNA149/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Thu Jul  3 14:33:01 BRT 2014
dtifit -k /MRI/Tracula-test/ESNA149/dmri/dwi.nii.gz -m /MRI/Tracula-test/ESNA149/dlabel/diff/lowb_brain_mask.nii.gz -r /MRI/Tracula-test/ESNA149/dmri/bvecs -b /MRI/Tracula-test/ESNA149/dmri/bvals -o /MRI/Tracula-test/ESNA149/dmri/dtifit
Error: data and bvals/bvecs do not contain the same number of entries
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 Thu Jul  3 14:33:06 BRT 2014