I'm trying to run the TRACULA software (fresurfer V 6.0) in the VM for FSL . I'm using the only elmo.2005 images but the program stops just at the middle of priors point.
In the follow the log file.
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Mon Sep 10 14:39:14 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
/usr/local/freesurfer/bin/trac-all
-prep -c /home/fsluser/usr_/local_/diffusion_tutorial/dmrirc.tutorial
Subject elmo.2005
SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
fsluser
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 4096
maxlocks unlimited
maxsignal 7172
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 1867264 702820 805888 12064 358556 947408
Swap: 3145724 506716 2639008
########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58
CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS:
User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS:
User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User:
fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58
CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58
CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User:
fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
fsluser
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 4096
maxlocks unlimited
maxsignal 7172
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 1867264 703636 772376 12064 391252 946564
Swap: 3145724 506712 2639012
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Sep 10 14:39:15 BST 2018
mri_convert --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No
INFO: Found 78 files in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory
INFO: found 70 files in series
INFO: loading series header info.
RunNo = 10
WARNING: Run 1 appears to be truncated
Files Found: 70, Files Expected (lRep+1): 120
FileName
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Trio
PatientName Trio_calib_002_run2
Date and time
StudyDate 20050905
StudyTime 100821.656000
SeriesTime 104226.748000
AcqTime 104209.522496
Acquisition parameters
PulseSeq ep_b0#0
Protocol DIFFUSION_HighRes
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 100
InversionTime -1
RepetitionTime 10100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 10
SeriesNo 11
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 70
SliceArraylSize 60
IsMosaic 1
ImgPos 1048.1801 1002.6923 -265.4914
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 60
Vc -0.9997 0.0244 0.0005
Vr -0.0238 -0.9764 0.2147
Vs 0.0057 0.2147 0.9767
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128 60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.99970 0.02376 -0.00570 -0.49480;
-0.02443 0.97638 -0.21466 -40.55519;
0.00047 0.21474 0.97667 12.50291;
0.00000 0.00000 0.00000 1.00000;
FileName
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Trio
PatientName Trio_calib_002_run2
Date and time
StudyDate 20050905
StudyTime 100821.656000
SeriesTime 104226.748000
AcqTime 104209.522496
Acquisition parameters
PulseSeq ep_b0#0
Protocol DIFFUSION_HighRes
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 100
InversionTime -1
RepetitionTime 10100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 10
SeriesNo 11
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 70
SliceArraylSize 60
IsMosaic 1
ImgPos 131.1612 149.7402 -72.6670
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 60
Vc -0.9997 0.0244 0.0005
Vr -0.0238 -0.9764 0.2147
Vs 0.0057 0.2147 0.9767
VolCenter 0.5005 40.7699 13.4796
TransferSyntaxUID unknown
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 1, correv =1, trarev = 0
Vs = 0.0057 0.214665 0.976671
INFO: no Siemens slice order reversal detected (good!).
TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999702, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
mri_probedicom --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat
cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvecs.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvals.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598)
normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474)
normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz...
INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying
INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
eddy_correct /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0000
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0001
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0002
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0003
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0004
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0005
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0006
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0007
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0008
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0009
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0010
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0011
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0012
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0013
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0014
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0015
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0016
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0017
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0018
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0019
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0020
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0021
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0022
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0023
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0024
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0025
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0026
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0027
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0028
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0029
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0030
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0031
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0032
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0033
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0034
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0035
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0036
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0037
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0038
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0039
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0040
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0041
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0042
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0043
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0044
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0045
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0046
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0047
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0048
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0049
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0050
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0051
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0052
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0053
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0054
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0055
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0056
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0057
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0058
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0059
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0060
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0061
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0062
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0063
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0064
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0065
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0066
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0067
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0068
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0069
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot
xfmrot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs
ln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/data.nii.gz
mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frames 0 1 2 3 4 5 6 7 8 9
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz...
mri_concat --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz --mean --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 10
Allocing output
Done allocing
nframes = 10
Computing mean across frames
Writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
bet /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff
#-------------------------------------
#@# Image quality assessment Mon Sep 10 14:50:58 BST 2018
/usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog
--bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog
--bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
Output motion measure file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt
Input transform file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog
Input DWI file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
Input b-value table: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
Low-b image intensity threshold: 139.4
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 70 volumes
Loading DWI volume series from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
Loading b-value table from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
Computing within-volume head motion measures
Done in 4.418 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Mon Sep 10 14:51:03 BST 2018
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz...
tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz --targ /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
--regheader --noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/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: --------------------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.00000 -0.00000 -0.00000 -0.00002;
0.00000 1.00000 0.00000 0.00004;
-0.00000 -0.00000 1.00000 0.99997;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
---- Input registration matrix --------
1.00000 -0.00000 -0.00000 -0.00002;
0.00000 1.00000 0.00000 0.00004;
-0.00000 -0.00000 1.00000 0.99997;
0.00000 0.00000 0.00000 1.00000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
1.00000 0.00000 0.00000 -0.00001;
0.00000 -0.00000 -1.00000 0.00004;
0.00000 1.00000 -0.00000 0.99997;
0.00000 0.00000 0.00000 1.00000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat
tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041
Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.log
Mon Sep 10 14:51:06 BST 2018
setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
/usr/local/freesurfer/bin/bbregister --s elmo.2005 --init-fsl --dti --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
--fslmat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
mri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...
fslregister --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fslregister.log
Mon Sep 10 14:51:12 BST 2018
--s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/fsluser/usr_/local_/diffusion_recons
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/fsluser/usr_/local_/diffusion_recons
mri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
--frame 0
mri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
--frame 0
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 0
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii...
Mov determinant is -8
/home/fsluser/usr_/local_/diffusion_recons
tkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat
--regheader --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0 --s elmo.2005 --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 2.00000 -60.00000;
0.00000 -2.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
0.99970 -0.02443 -0.00047 3.11760;
0.00570 0.21466 0.97667 2.25865;
-0.02376 -0.97638 0.21474 -1.16418;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
---- Input registration matrix --------
0.99970 -0.02443 -0.00047 3.11760;
0.00570 0.21466 0.97667 2.25865;
-0.02376 -0.97638 0.21474 -1.16418;
0.00000 0.00000 0.00000 1.00000;
Determinant 1
subject = elmo.2005
RegMat ---------------------------
0.99970 -0.02443 -0.00047 3.11760;
0.00570 0.21466 0.97667 2.25865;
-0.02376 -0.97638 0.21474 -1.16418;
0.00000 0.00000 0.00000 1.00000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -8, ref det = -1
Mon Sep 10 14:51:17 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
flirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch
-init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0
Mon Sep 10 14:51:23 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
flirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--fslreg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
0.99918 -0.04042 0.00180 7.99378;
0.01127 0.23516 -0.97189 154.31700;
0.03886 0.97112 0.23542 -17.03460;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
Tmov: --------------------
-2.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 2.00000 -60.00000;
0.00000 -2.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
0.99918 -0.03886 0.01127 2.75252;
-0.00180 0.23542 0.97189 -0.06236;
-0.04042 -0.97112 0.23516 -1.80609;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
---- Input registration matrix --------
0.99918 -0.03886 0.01127 2.75252;
-0.00180 0.23542 0.97189 -0.06236;
-0.04042 -0.97112 0.23516 -1.80609;
0.00000 0.00000 0.00000 1.00000;
Determinant 0.999999
subject = elmo.2005
RegMat ---------------------------
0.99918 -0.03886 0.01127 2.75252;
-0.00180 0.23542 0.97189 -0.06236;
-0.04042 -0.97112 0.23516 -1.80609;
0.00000 0.00000 0.00000 1.00000;
(standard_in) 1: syntax error
Started at Mon Sep 10 14:51:12 BST 2018
Ended at Mon Sep 10 14:51:41 BST 2018
fslregister Done
To check results, run:
tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--surf orig
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
--out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
subject elmo.2005
dof 6
outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp trilinear (1)
frame 0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1537118316
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
0.99918 -0.03886 0.01127 2.75252;
-0.00180 0.23542 0.97189 -0.06236;
-0.04042 -0.97112 0.23516 -1.80609;
0.00000 0.00000 0.00000 1.00000;
Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0 -25.0 -25.0 -25.0 0.985304
1 -25.0 -25.0 25.0 1.003463
2 -25.0 25.0 -25.0 0.981149
3 -25.0 25.0 25.0 1.010608
4 25.0 -25.0 -25.0 0.997072
5 25.0 -25.0 25.0 1.010833
6 25.0 25.0 -25.0 0.981523
7 25.0 25.0 25.0 1.019362
REL: 8 0.481295 7.989313 0.998664 rel = 0.481938
Initial costs ----------------
Number of surface hits 2679
WM Intensity 208.1729 +/- 115.2740
Ctx Intensity 275.5693 +/- 149.3314
Pct Contrast 23.8307 +/- 42.4267
Cost 0.4813
RelCost 0.4819
------------------------------------
Brute force preopt -4 4 4, n = 729
0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9886 0.9886 0.0
1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9625 0.9625 0.0
2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9370 0.9370 0.0
6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9237 0.9237 0.0
7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8538 0.8538 0.0
97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.8210 0.8210 0.0
123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.7789 0.7789 0.0
124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7606 0.7606 0.0
363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7168 0.7168 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4813 0.4813 0.0
Brute Force --------------------------
Min cost was 0.481295
Number of iterations 729
Search time 1.611000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 0.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
nparams 6
maxfev 36
ftol 0.000100
linmin_xtol_ 0.001000
powell nthiter 0: fret = 0.481295
7 0.135 0.000 0.000 0.000 0.000 0.000 0.4779112049
10 0.122 0.000 0.000 0.000 0.000 0.000 0.4778248409
12 0.123 0.000 0.000 0.000 0.000 0.000 0.4778223804
25 0.123 -0.044 0.000 0.000 0.000 0.000 0.4778011390
29 0.123 -0.036 0.000 0.000 0.000 0.000 0.4777963222
31 0.123 -0.039 0.000 0.000 0.000 0.000 0.4777931744
35 0.123 -0.039 1.000 0.000 0.000 0.000 0.4654924758
44 0.123 -0.039 1.033 0.000 0.000 0.000 0.4649766994
45 0.123 -0.039 1.037 0.000 0.000 0.000 0.4649588157
47 0.123 -0.039 1.039 0.000 0.000 0.000 0.4649545250
54 0.123 -0.039 1.039 -0.618 0.000 0.000 0.4613594586
56 0.123 -0.039 1.039 -0.356 0.000 0.000 0.4606742453
57 0.123 -0.039 1.039 -0.432 0.000 0.000 0.4592808449
58 0.123 -0.039 1.039 -0.476 0.000 0.000 0.4591395480
59 0.123 -0.039 1.039 -0.466 0.000 0.000 0.4588285780
60 0.123 -0.039 1.039 -0.455 0.000 0.000 0.4586162323
62 0.123 -0.039 1.039 -0.452 0.000 0.000 0.4586004888
63 0.123 -0.039 1.039 -0.451 0.000 0.000 0.4586003764
75 0.123 -0.039 1.039 -0.451 -0.010 0.000 0.4585257072
76 0.123 -0.039 1.039 -0.451 -0.014 0.000 0.4585225156
77 0.123 -0.039 1.039 -0.451 -0.013 0.000 0.4585219959
87 0.123 -0.039 1.039 -0.451 -0.013 0.032 0.4585072286
88 0.123 -0.039 1.039 -0.451 -0.013 0.018 0.4584264964
89 0.123 -0.039 1.039 -0.451 -0.013 0.016 0.4584253499
90 0.123 -0.039 1.039 -0.451 -0.013 0.015 0.4584251210
powell nthiter 1: fret = 0.458425
99 -0.030 -0.039 1.039 -0.451 -0.013 0.015 0.4548510808
100 -0.071 -0.039 1.039 -0.451 -0.013 0.015 0.4543073001
104 -0.062 -0.039 1.039 -0.451 -0.013 0.015 0.4542563468
106 -0.063 -0.039 1.039 -0.451 -0.013 0.015 0.4542556740
113 -0.063 -0.657 1.039 -0.451 -0.013 0.015 0.4514610163
115 -0.063 -0.401 1.039 -0.451 -0.013 0.015 0.4419651219
116 -0.063 -0.368 1.039 -0.451 -0.013 0.015 0.4417822150
118 -0.063 -0.381 1.039 -0.451 -0.013 0.015 0.4415713539
129 -0.063 -0.381 0.949 -0.451 -0.013 0.015 0.4409935232
131 -0.063 -0.381 0.983 -0.451 -0.013 0.015 0.4399692941
132 -0.063 -0.381 0.989 -0.451 -0.013 0.015 0.4399364486
133 -0.063 -0.381 0.991 -0.451 -0.013 0.015 0.4399362054
144 -0.063 -0.381 0.991 -0.435 -0.013 0.015 0.4396884912
146 -0.063 -0.381 0.991 -0.436 -0.013 0.015 0.4396863031
159 -0.063 -0.381 0.991 -0.436 -0.012 0.015 0.4396857374
168 -0.063 -0.381 0.991 -0.436 -0.012 0.002 0.4396353849
169 -0.063 -0.381 0.991 -0.436 -0.012 0.001 0.4396340069
170 -0.063 -0.381 0.991 -0.436 -0.012 -0.002 0.4396327392
172 -0.063 -0.381 0.991 -0.436 -0.012 -0.001 0.4396322829
powell nthiter 2: fret = 0.439632
184 -0.064 -0.381 0.991 -0.436 -0.012 -0.001 0.4396101542
185 -0.070 -0.381 0.991 -0.436 -0.012 -0.001 0.4395798553
208 -0.070 -0.381 0.977 -0.436 -0.012 -0.001 0.4394650593
210 -0.070 -0.381 0.979 -0.436 -0.012 -0.001 0.4394625826
222 -0.070 -0.381 0.979 -0.431 -0.012 -0.001 0.4394569675
223 -0.070 -0.381 0.979 -0.433 -0.012 -0.001 0.4394533231
234 -0.070 -0.381 0.979 -0.433 -0.004 -0.001 0.4394149746
235 -0.070 -0.381 0.979 -0.433 -0.006 -0.001 0.4394125073
powell nthiter 3: fret = 0.439413
259 -0.069 -0.381 0.979 -0.433 -0.006 -0.001 0.4394122592
269 -0.069 -0.380 0.979 -0.433 -0.006 -0.001 0.4394115605
281 -0.069 -0.380 0.975 -0.433 -0.006 -0.001 0.4393971568
305 -0.069 -0.380 0.975 -0.433 -0.004 -0.001 0.4393957905
318 -0.069 -0.380 0.975 -0.433 -0.004 -0.003 0.4393945423
Powell done niters = 3
Computing relative cost
0 -25.0 -25.0 -25.0 0.981197
1 -25.0 -25.0 25.0 1.000288
2 -25.0 25.0 -25.0 0.994687
3 -25.0 25.0 25.0 1.000546
4 25.0 -25.0 -25.0 1.008915
5 25.0 -25.0 25.0 1.016643
6 25.0 25.0 -25.0 0.996728
7 25.0 25.0 25.0 1.026021
REL: 8 0.439395 8.025025 1.003128 rel = 0.438024
Number of iterations 3
Min cost was 0.439395
Number of FunctionCalls 320
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.933000 sec
Parameters at optimum (transmm) -0.06893 -0.37986 0.97505
Parameters at optimum (rotdeg) -0.43286 -0.00427 -0.00320
Final costs ----------------
Number of surface hits 2680
WM Intensity 204.6878 +/- 112.1423
Ctx Intensity 275.3361 +/- 147.5540
Pct Contrast 25.6014 +/- 41.7909
Cost 0.4394
RelCost 0.4819
Reg at min cost was
0.99918 -0.03878 0.01130 2.68372;
-0.00216 0.22808 0.97364 -0.45602;
-0.04033 -0.97287 0.22781 -0.83031;
0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat, type = 14
Original Reg
0.99918 -0.03886 0.01127 2.75252;
-0.00180 0.23542 0.97189 -0.06236;
-0.04042 -0.97112 0.23516 -1.80609;
0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg
-0.00000 -0.00009 -0.00004 0.06880;
0.00036 0.00734 -0.00175 0.39366;
-0.00009 0.00175 0.00735 -0.97578;
0.00000 0.00000 0.00000 0.00000;
Computing change in lh position
LH rmsDiffMean 1.025998
Computing change in rh position
Surface-RMS-Diff-mm 1.020289 0.188730 1.405123
mri_segreg done
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
--out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost
--dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat
--gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
--out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost
--dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat
--gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
subject elmo.2005
dof 6
outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp trilinear (1)
frame 0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1537544095
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
0.99918 -0.03878 0.01130 2.68372;
-0.00216 0.22808 0.97364 -0.45602;
-0.04033 -0.97287 0.22781 -0.83031;
0.00000 0.00000 0.00000 1.00000;
Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0 -25.0 -25.0 -25.0 0.994360
1 -25.0 -25.0 25.0 1.009170
2 -25.0 25.0 -25.0 1.028103
3 -25.0 25.0 25.0 0.993501
4 25.0 -25.0 -25.0 1.009256
5 25.0 -25.0 25.0 1.005871
6 25.0 25.0 -25.0 0.984198
7 25.0 25.0 25.0 1.020678
REL: 8 0.457378 8.045138 1.005642 rel = 0.454812
Initial costs ----------------
Number of surface hits 267146
WM Intensity 206.3564 +/- 113.7131
Ctx Intensity 277.7282 +/- 152.7763
Pct Contrast 25.3732 +/- 42.7352
Cost 0.4574
RelCost 0.4548
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4515 0.4515 0.0
3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4497 0.4497 0.0
6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.4462 0.4462 0.0
12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.4461 0.4461 0.0
21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.4457 0.4457 0.0
24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.4444 0.4444 0.0
36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.4435 0.4435 0.0
54 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.4427 0.4427 0.0
63 -0.1000 -0.1000 0.1000 0.0000 -0.1000 -0.1000 0.4415 0.4415 0.0
258 0.0000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.4412 0.4412 0.0
282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.4404 0.4404 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4394 0.4394 0.0
Brute Force --------------------------
Min cost was 0.439395
Number of iterations 729
Search time 1.510000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 0.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
nparams 6
maxfev 36
ftol 0.000000
linmin_xtol_ 0.001000
powell nthiter 0: fret = 0.457378
7 0.151 0.000 0.000 0.000 0.000 0.000 0.4567799639
9 0.149 0.000 0.000 0.000 0.000 0.000 0.4567796745
10 0.148 0.000 0.000 0.000 0.000 0.000 0.4567792997
11 0.142 0.000 0.000 0.000 0.000 0.000 0.4567788014
12 0.144 0.000 0.000 0.000 0.000 0.000 0.4567786136
20 0.144 -0.113 0.000 0.000 0.000 0.000 0.4562133870
21 0.144 -0.102 0.000 0.000 0.000 0.000 0.4562102480
36 0.144 -0.102 0.005 0.000 0.000 0.000 0.4562068973
40 0.144 -0.102 0.016 0.000 0.000 0.000 0.4562045472
41 0.144 -0.102 0.015 0.000 0.000 0.000 0.4562045116
42 0.144 -0.102 0.014 0.000 0.000 0.000 0.4562044856
51 0.144 -0.102 0.014 -0.115 0.000 0.000 0.4555371966
53 0.144 -0.102 0.014 -0.123 0.000 0.000 0.4555367143
55 0.144 -0.102 0.014 -0.127 0.000 0.000 0.4555352434
57 0.144 -0.102 0.014 -0.125 0.000 0.000 0.4555347108
58 0.144 -0.102 0.014 -0.124 0.000 0.000 0.4555344977
65 0.144 -0.102 0.014 -0.124 -0.030 0.000 0.4553394364
67 0.144 -0.102 0.014 -0.124 -0.071 0.000 0.4552874340
68 0.144 -0.102 0.014 -0.124 -0.079 0.000 0.4552792468
69 0.144 -0.102 0.014 -0.124 -0.101 0.000 0.4552413108
71 0.144 -0.102 0.014 -0.124 -0.102 0.000 0.4552404588
72 0.144 -0.102 0.014 -0.124 -0.104 0.000 0.4552395026
82 0.144 -0.102 0.014 -0.124 -0.104 -0.293 0.4522931503
83 0.144 -0.102 0.014 -0.124 -0.104 -0.291 0.4522918016
powell nthiter 1: fret = 0.452292
95 0.133 -0.102 0.014 -0.124 -0.104 -0.291 0.4522544133
96 0.090 -0.102 0.014 -0.124 -0.104 -0.291 0.4522221844
98 0.105 -0.102 0.014 -0.124 -0.104 -0.291 0.4522023296
99 0.106 -0.102 0.014 -0.124 -0.104 -0.291 0.4522022033
107 0.106 -0.174 0.014 -0.124 -0.104 -0.291 0.4516567107
109 0.106 -0.189 0.014 -0.124 -0.104 -0.291 0.4516347638
110 0.106 -0.190 0.014 -0.124 -0.104 -0.291 0.4516342016
111 0.106 -0.195 0.014 -0.124 -0.104 -0.291 0.4516309356
114 0.106 -0.194 0.014 -0.124 -0.104 -0.291 0.4516305236
122 0.106 -0.194 0.022 -0.124 -0.104 -0.291 0.4515978255
123 0.106 -0.194 0.075 -0.124 -0.104 -0.291 0.4515177696
125 0.106 -0.194 0.068 -0.124 -0.104 -0.291 0.4515073442
126 0.106 -0.194 0.060 -0.124 -0.104 -0.291 0.4515053860
127 0.106 -0.194 0.062 -0.124 -0.104 -0.291 0.4515048438
137 0.106 -0.194 0.062 -0.144 -0.104 -0.291 0.4514614868
138 0.106 -0.194 0.062 -0.149 -0.104 -0.291 0.4514588764
147 0.106 -0.194 0.062 -0.149 -0.008 -0.291 0.4511294521
148 0.106 -0.194 0.062 -0.149 -0.013 -0.291 0.4511263788
149 0.106 -0.194 0.062 -0.149 -0.018 -0.291 0.4511189418
150 0.106 -0.194 0.062 -0.149 -0.051 -0.291 0.4510869949
152 0.106 -0.194 0.062 -0.149 -0.038 -0.291 0.4510857743
153 0.106 -0.194 0.062 -0.149 -0.044 -0.291 0.4510847166
154 0.106 -0.194 0.062 -0.149 -0.043 -0.291 0.4510847161
164 0.106 -0.194 0.062 -0.149 -0.043 -0.296 0.4510831507
165 0.106 -0.194 0.062 -0.149 -0.043 -0.297 0.4510831286
powell nthiter 2: fret = 0.451083
174 0.099 -0.194 0.062 -0.149 -0.043 -0.297 0.4510503240
176 0.077 -0.194 0.062 -0.149 -0.043 -0.297 0.4510213872
178 0.080 -0.194 0.062 -0.149 -0.043 -0.297 0.4510195676
180 0.083 -0.194 0.062 -0.149 -0.043 -0.297 0.4510186920
201 0.084 -0.194 0.073 -0.149 -0.043 -0.297 0.4510115521
203 0.084 -0.194 0.072 -0.149 -0.043 -0.297 0.4510115142
215 0.084 -0.194 0.072 -0.148 -0.043 -0.297 0.4510112026
223 0.084 -0.194 0.072 -0.148 0.005 -0.297 0.4509468373
226 0.084 -0.194 0.072 -0.148 0.006 -0.297 0.4509467632
236 0.084 -0.194 0.072 -0.148 0.007 -0.307 0.4509344989
242 0.062 -0.194 0.082 -0.147 0.057 -0.314 0.4509154629
powell nthiter 3: fret = 0.450934
249 0.075 -0.194 0.072 -0.148 0.007 -0.306 0.4508891386
251 0.050 -0.194 0.072 -0.148 0.007 -0.306 0.4508574823
254 0.049 -0.194 0.072 -0.148 0.007 -0.306 0.4508574680
255 0.048 -0.194 0.072 -0.148 0.007 -0.306 0.4508572280
258 0.046 -0.194 0.072 -0.148 0.007 -0.306 0.4508570447
268 0.047 -0.189 0.072 -0.148 0.007 -0.306 0.4508534999
279 0.047 -0.189 0.063 -0.148 0.007 -0.306 0.4508490816
280 0.047 -0.189 0.061 -0.148 0.007 -0.306 0.4508484187
282 0.047 -0.189 0.057 -0.148 0.007 -0.306 0.4508481470
283 0.047 -0.189 0.058 -0.148 0.007 -0.306 0.4508481128
294 0.047 -0.189 0.058 -0.147 0.007 -0.306 0.4508480229
302 0.047 -0.189 0.058 -0.147 0.027 -0.306 0.4508401595
303 0.047 -0.189 0.058 -0.147 0.022 -0.306 0.4508368880
304 0.047 -0.189 0.058 -0.147 0.020 -0.306 0.4508368307
306 0.047 -0.189 0.058 -0.147 0.021 -0.306 0.4508366606
314 0.047 -0.189 0.058 -0.147 0.021 -0.330 0.4507887096
317 0.047 -0.189 0.058 -0.147 0.021 -0.331 0.4507886723
powell nthiter 4: fret = 0.450789
327 0.040 -0.189 0.058 -0.147 0.021 -0.331 0.4507863478
338 0.040 -0.202 0.058 -0.147 0.021 -0.331 0.4507856198
339 0.040 -0.196 0.058 -0.147 0.021 -0.331 0.4507778523
340 0.040 -0.195 0.058 -0.147 0.021 -0.331 0.4507778168
350 0.040 -0.195 0.057 -0.147 0.021 -0.331 0.4507776939
359 0.040 -0.195 0.057 -0.140 0.021 -0.331 0.4507760945
360 0.040 -0.195 0.057 -0.141 0.021 -0.331 0.4507753773
368 0.040 -0.195 0.057 -0.141 0.034 -0.331 0.4507701303
379 0.040 -0.195 0.057 -0.141 0.034 -0.342 0.4507598537
381 0.040 -0.195 0.057 -0.141 0.034 -0.341 0.4507597243
powell nthiter 5: fret = 0.450760
392 0.036 -0.195 0.057 -0.141 0.034 -0.341 0.4507576686
393 0.035 -0.195 0.057 -0.141 0.034 -0.341 0.4507573174
395 0.034 -0.195 0.057 -0.141 0.034 -0.341 0.4507572876
404 0.034 -0.194 0.057 -0.141 0.034 -0.341 0.4507572313
413 0.034 -0.194 0.052 -0.141 0.034 -0.341 0.4507558538
414 0.034 -0.194 0.050 -0.141 0.034 -0.341 0.4507554828
427 0.034 -0.194 0.050 -0.140 0.034 -0.341 0.4507551369
428 0.034 -0.194 0.050 -0.139 0.034 -0.341 0.4507551204
437 0.034 -0.194 0.050 -0.139 0.033 -0.341 0.4507549405
450 0.034 -0.194 0.050 -0.139 0.033 -0.343 0.4507547248
powell nthiter 6: fret = 0.450755
480 0.035 -0.194 0.049 -0.139 0.033 -0.343 0.4507544467
481 0.035 -0.194 0.046 -0.139 0.033 -0.343 0.4507537921
483 0.035 -0.194 0.043 -0.139 0.033 -0.343 0.4507536567
484 0.035 -0.194 0.044 -0.139 0.033 -0.343 0.4507536554
493 0.035 -0.194 0.044 -0.138 0.033 -0.343 0.4507533174
494 0.035 -0.194 0.044 -0.137 0.033 -0.343 0.4507532305
503 0.035 -0.194 0.044 -0.137 0.032 -0.343 0.4507531155
514 0.035 -0.194 0.044 -0.137 0.032 -0.342 0.4507531014
516 0.036 -0.194 0.039 -0.135 0.031 -0.341 0.4507523120
530 0.036 -0.194 0.039 -0.135 0.031 -0.341 0.4507522623
powell nthiter 7: fret = 0.450752
542 0.035 -0.194 0.039 -0.135 0.031 -0.341 0.4507520844
552 0.035 -0.195 0.039 -0.135 0.031 -0.341 0.4507516977
563 0.035 -0.195 0.039 -0.135 0.031 -0.342 0.4507516535
591 0.035 -0.195 0.037 -0.134 0.029 -0.341 0.4507515057
592 0.035 -0.195 0.036 -0.134 0.029 -0.341 0.4507514870
593 0.035 -0.195 0.035 -0.134 0.029 -0.341 0.4507513959
powell nthiter 8: fret = 0.450751
612 0.034 -0.195 0.035 -0.134 0.029 -0.341 0.4507512254
622 0.034 -0.196 0.035 -0.134 0.029 -0.341 0.4507510902
powell nthiter 9: fret = 0.450751
Powell done niters = 9
Computing relative cost
0 -25.0 -25.0 -25.0 0.993321
1 -25.0 -25.0 25.0 1.009943
2 -25.0 25.0 -25.0 1.031408
3 -25.0 25.0 25.0 0.987702
4 25.0 -25.0 -25.0 1.008434
5 25.0 -25.0 25.0 1.004908
6 25.0 25.0 -25.0 0.987196
7 25.0 25.0 25.0 1.021866
REL: 8 0.450751 8.044778 1.005597 rel = 0.448242
Number of iterations 9
Min cost was 0.450751
Number of FunctionCalls 741
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 40.719000 sec
Parameters at optimum (transmm) 0.03411 -0.19584 0.03511
Parameters at optimum (rotdeg) -0.13370 0.02919 -0.34094
Final costs ----------------
Number of surface hits 267260
WM Intensity 205.3026 +/- 114.1749
Ctx Intensity 276.2650 +/- 150.7064
Pct Contrast 25.5313 +/- 42.4962
Cost 0.4508
RelCost 0.4548
Reg at min cost was
0.99913 -0.03793 0.01722 2.71464;
-0.00820 0.22604 0.97408 -0.66975;
-0.04084 -0.97338 0.22553 -0.79550;
0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat, type = 14
Original Reg
0.99918 -0.03878 0.01130 2.68372;
-0.00216 0.22808 0.97364 -0.45602;
-0.04033 -0.97287 0.22781 -0.83031;
0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg
0.00005 -0.00085 -0.00591 -0.03092;
0.00604 0.00204 -0.00044 0.21373;
0.00050 0.00051 0.00228 -0.03481;
0.00000 0.00000 0.00000 0.00000;
Computing change in lh position
LH rmsDiffMean 0.210903
Computing change in rh position
Surface-RMS-Diff-mm 0.304233 0.140570 0.625049
mri_segreg done
MinCost: 0.450751 205.302557 276.265001 25.531318
tkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
--noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz
reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
0.99913 -0.03793 0.01722 2.71464;
-0.00820 0.22604 0.97408 -0.66975;
-0.04084 -0.97338 0.22553 -0.79550;
0.00000 0.00000 0.00000 1.00000;
float2int = 0
---------------------------------------
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz
Tmov: --------------------
-2.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 2.00000 -60.00000;
0.00000 -2.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
0.99913 -0.03793 0.01722 2.71464;
-0.00820 0.22604 0.97408 -0.66975;
-0.04084 -0.97338 0.22553 -0.79550;
0.00000 0.00000 0.00000 1.00000;
Determinant 0.999999
subject = elmo.2005
RegMat ---------------------------
0.99913 -0.03793 0.01722 2.71464;
-0.00820 0.22604 0.97408 -0.66975;
-0.04084 -0.97338 0.22553 -0.79550;
0.00000 0.00000 0.00000 1.00000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -8, ref det = -1
Cleaning up
Started at Mon Sep 10 14:51:06 BST 2018
Ended at Mon Sep 10 14:52:47 BST 2018
BBR-Run-Time-Sec 101
bbregister Done
To check results, run:
tkregisterfv --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
--surfs
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration Mon Sep 10 14:52:47 BST 2018
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_mni.nii.gz
-omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anat.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Mon Sep 10 14:54:35 BST 2018
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/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
fstart = 0, fend = 0, nframes = 1
Found 466816 values in range
Counting number of voxels in first frame
Found 466816 voxels in final mask
Count: 466816 466816.000000 16777216 2.782440
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match
16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28
--match 60 --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/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
fstart = 0, fend = 0, nframes = 1
Found 496933 values in range
Counting number of voxels in first frame
Found 496933 voxels in final mask
Count: 496933 496933.000000 16777216 2.961951
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
0 4
1 43
binval 0
binvalnot 1
fstart = 0, fend = 0, nframes = 1
Found 23114 values in range
Counting number of voxels in first frame
Found 23114 voxels in final mask
Count: 23114 23114.000000 16777216 0.137770
mri_binarize done
mri_aparc2aseg --s elmo.2005 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
subject elmo.2005
outvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/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
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.white
Reading lh pial surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.pial
Loading lh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/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
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.white
Reading rh pial surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.pial
Loading rh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/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 /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz
Loading filled from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
-------------------------
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 = 1019533
Used brute-force search on 0 voxels
Fixing Parahip LH WM
Found 1 clusters
0 k 889.000000
Fixing Parahip RH WM
Found 1 clusters
0 k 714.000000
Writing output aseg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min 1000
max 2999
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 577605 values in range
Counting number of voxels in first frame
Found 577605 voxels in final mask
Count: 577605 577605.000000 16777216 3.442794
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min 1000
max 4999
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 848289 values in range
Counting number of voxels in first frame
Found 848289 voxels in final mask
Count: 848289 848289.000000 16777216 5.056196
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
0 16
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 21835 values in range
Counting number of voxels in first frame
Found 21835 voxels in final mask
Count: 21835 21835.000000 16777216 0.130147
mri_binarize done
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz -add /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz -mul /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/notventricles.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm+bs.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt
nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046
-rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_snr.txt
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
-out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Mon Sep 10 15:00:40 BST 2018
dtifit -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -m /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
-r /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs -b /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals -o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit
0 128 0 128 0 60
0 slices processed
1 slices processed
2 slices processed
3 slices processed
4 slices processed
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53 slices processed
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55 slices processed
56 slices processed
57 slices processed
58 slices processed
59 slices processed
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_FA.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L1.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L1.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L2.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L2.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L3.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L3.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MD.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MD.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MO.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MO.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_S0.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_S0.bbr.nii.gz
-applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
#-------------------------------------
#@# Priors Mon Sep 10 15:00:50 BST 2018
/usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr
lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr
rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk
dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk
dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask
16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz
dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz
dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz
dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz
dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline /usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr
lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr
rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk
dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk
dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask
16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz
dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz
dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz
dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz
dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir
/home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
sysname Linux
hostname localhost.localdomain
machine x86_64
user fsluser
Output directory: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni
Output directory in test subject's space: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr
fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.elmo.2005.26311.txt
Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk
dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk
Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz
dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz
FA map for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz
Affine registration from atlas to base for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat
Number of control points for initial spline: 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5
Exclude previously chosen center streamlines: 0
Use truncated streamlines: 1
Loading brain mask of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz
Loading FA map of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz
Loading affine registration from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.bbr.trk
INFO: Rejected 1094 streamlines for straying off mask
INFO: Rejected 73 streamlines for reversing direction
INFO: Rejected 17 streamlines as length outliers
INFO: Have 7248 total streamlines (min/mean/max length: 59/99/139)
Loading segmentation from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/cortex+2mm.nii.gz
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Sep 10 15:07:07 BST 2018