Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64).
OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 ---------- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. ------------------------------------------------------------------- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway
0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 0 0 0
0 -0.20377 0.19788 0.40243 -0.40388 -0.20233 -0.85342 -0.73137 -0.40767 -0.73256 -0.65079 -0.32244 -0.32447 -0.65033 -0.97858 -0.85456 0.00073292 0.0031555 0.65459 0.32946 0.19801 0.20431 0.65167 0.32436 0.20046 0.40388 0.73222 0.72893 0.85265 0.85748 0.97941 -0.20383 0.19838 0.40215 -0.40386 -0.20227 -0.85391 -0.73143 -0.40738 -0.73222 -0.65118 -0.32277 -0.32447 -0.65021 -0.97877 -0.85407 0.0010746 0.0026895 0.65409 0.32975 0.19853 0.20382 0.65198 0.3244 0.20042 0.40386 0.73188 0.7289 0.85313 0.85703 0.97941 0 0 0 0 0.51899 0.51978 0.17539 0.73086 0.94157 0.51794 0.51937 0.17571 0.17545 0.72984 0.94086 0.51874 0.51945 0.17617 0.17537 0.73084 0.94144 0.51829 0.51954 -0.17606 0.17598 0.72974 0.94079 0.94034 0.73086 0.17554 0.51833 0.51851 0.17573 0.17521 0.51781 0.51844 0.17453 0.72992 0.9411 0.51692 0.51814 0.17485 0.17442 0.72913 0.94057 0.51783 0.51815 0.17474 0.17462 0.72996 0.94104 0.51757 0.51819 -0.17448 0.17457 0.72915 0.94064 0.94004 0.72992 0.17443 0.51753 0.51749 0.17457 0.17459 0 0 0 0 0.83013 0.83106 0.89849 0.5502 0.26929 0.058462 0.44199 0.89606 0.6577 -0.20929 -0.104 -0.79096 -0.55429 -0.10651 -0.48884 -0.68255 -0.33718 -0.55035 -0.78837 0.96426 -0.96296 -0.20688 -0.098539 0.27491 0.5502 0.65806 0.44721 0.064332 -0.48358 -0.1003 0.83086 0.83178 0.89878 0.55146 0.27096 0.060296 0.44333 0.89636 0.65836 -0.21059 -0.10562 -0.79157 -0.55565 -0.10708 -0.48997 -0.68349 -0.33829 -0.55161 -0.78914 0.96444 -0.96332 -0.20797 -0.099828 0.27597 0.55146 0.65872 0.44819 0.066168 -0.48479 -0.10137 0 0 0
bvals
Description: Binary data
bvec
Description: Binary data
lø. 02. juli 09:47:59 +0200 2016
/media/lmr2/subjects/DTI
/usr/local/freesurfer/bin/trac-all
-c dmric_test_mars2015 -prep
Subject 4_FS
SUBJECTS_DIR /media/lmr2/subjects/DTI
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
lmr
dmed4870
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 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 31844
maxlocks unlimited
maxsignal 31844
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 8173516 7744040 429476 161932 452448 2369504
-/+ buffers/cache: 4922088 3251428
Swap: 8385532 230000 8155532
########################################
Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/02-07:47:59-GMT BuildTimeStamp: May 22 2014 21:05:21 CVS: User: lmr Machine: dmed4870 Platform: Linux PlatformVersion: 3.19.0-31-generic CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
lmr
dmed4870
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 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 31844
maxlocks unlimited
maxsignal 31844
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 8173516 7746712 426804 161932 452448 2369504
-/+ buffers/cache: 4924760 3248756
Swap: 8385532 230000 8155532
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections lø. 02. juli 09:47:59 +0200 2016
mri_convert /media/lmr2/subjects/DTI/4/5/1.dcm /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz
mri_convert /media/lmr2/subjects/DTI/4/5/1.dcm /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/4/5/1.dcm...
crypt_gkey = FS8AfEXkNgFJk
Getting Series No
INFO: Found 71 files in /media/lmr2/subjects/DTI/4/5
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 64 files in series
INFO: loading series header info.
RunNo = 4
WARNING: Run 1 appears to be truncated
Files Found: 64, Files Expected (lRep+1): 1
FileName /media/lmr2/subjects/DTI/4/5/1.dcm
Identification
NumarisVer syngo MR D13
ScannerModel Skyra
PatientName Lavf004
Date and time
StudyDate 20130628
StudyTime 101427.272000
SeriesTime 103147.149000
AcqTime 102838.205000
Acquisition parameters
PulseSeq *ep_b0
Protocol DTI/DKI
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 8800
PhEncFOV 240
ReadoutFOV 240
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 64
SliceArraylSize 60
IsMosaic 1
ImgPos 959.8146 952.4999 -76.8872
VolRes 2.5000 2.5000 2.5000
VolDim 96 96 60
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: ( 96 96 60), nframes = 64, ismosaic=1
Could not parse NUMARIS version string syngo MR D13
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 8800, TR = 8800 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /media/lmr2/subjects/DTI/4/5/1.dcm
Identification
NumarisVer syngo MR D13
ScannerModel Skyra
PatientName Lavf004
Date and time
StudyDate 20130628
StudyTime 101427.272000
SeriesTime 103147.149000
AcqTime 102838.205000
Acquisition parameters
PulseSeq *ep_b0
Protocol DTI/DKI
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 8800
PhEncFOV 240
ReadoutFOV 240
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 64
SliceArraylSize 60
IsMosaic 1
ImgPos 119.8146 112.5000 -76.8872
VolRes 2.5000 2.5000 2.5000
VolDim 96 96 60
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter -0.1854 -7.5000 -1.8872
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=8800.00, TE=95.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
mri_probedicom --i /media/lmr2/subjects/DTI/4/5/1.dcm > /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dcminfo.dat
cp /media/lmr2/subjects/DTI/bvec_rows.csv /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvecs
cp /media/lmr2/subjects/DTI/bvals_rows.csv /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvals
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs.tmp /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvecs
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals.tmp /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvals
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 15.625
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz x -y z /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.nii.gz
INFO: found /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.mghdti.bvecs /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.mghdti.bvals /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals
eddy_correct /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig_flip.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz 0
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0000
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0001
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0002
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0003
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0004
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0005
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0006
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0007
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0008
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0009
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0010
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0011
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0012
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0013
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0014
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0015
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0016
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0017
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0018
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0019
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0020
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0021
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0022
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0023
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0024
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0025
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0026
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0027
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0028
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0029
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0030
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0031
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0032
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0033
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0034
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0035
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0036
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0037
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0038
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0039
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0040
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0041
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0042
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0043
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0044
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0045
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0046
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0047
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0048
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0049
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0050
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0051
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0052
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0053
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0054
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0055
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0056
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0057
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0058
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0059
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0060
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0061
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0062
processing /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_tmp0063
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs.norot
xfmrot /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.ecclog /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs.norot /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs
ln -sf /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/data.nii.gz
mri_convert --frame 0 61 62 63 /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz
mri_convert --frame 0 61 62 63 /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 0 61 62 63
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
mri_concat --i /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz --mean --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Computing mean across frames
Writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz
bet /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb_brain_mask.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff
#-------------------------------------
#@# Image quality assessment lø. 02. juli 09:52:27 +0200 2016
/usr/local/freesurfer/bin/dmri_motion --dwi /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz --mat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.ecclog --bval /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals --out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_motion.txt
cwd /media/lmr2/subjects/DTI
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz --mat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.ecclog --bval /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals --out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_motion.txt
sysname Linux
hostname dmed4870
machine x86_64
user lmr
Output motion measure file: /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_motion.txt
Input transform file: /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.ecclog
Input DWI file: /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz
Input b-value table: /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals
Low-b image intensity threshold: 100
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 64 volumes
Loading DWI volume series from /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_orig.nii.gz
Loading b-value table from /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals
Computing within-volume head motion measures
Done in 2.996 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration lø. 02. juli 09:52:30 +0200 2016
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brain.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brain.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/4_FS/mri/brain.mgz...
crypt_gkey = FS8AfEXkNgFJk
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, 6.33299e-08, 5.7742e-08)
j_ras = (-4.84288e-08, 5.82077e-10, -1)
k_ras = (-1.49012e-08, 1, -4.65661e-10)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz
tkregister2 --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz --targ /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2anat.mat --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target volume /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz
movable volume /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz
reg file /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2anatorig.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.000 0.000 -0.000 -0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 1.000;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 -0.000 -0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 1.000;
0.000 0.000 0.000 1.000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
1.000 0.000 0.000 -0.000;
0.000 -0.000 -1.000 0.000;
0.000 1.000 0.000 1.000;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2anatorig.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2anat.mat
Log file is /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat.log
lø. 02. juli 09:52:32 +0200 2016
setenv SUBJECTS_DIR /media/lmr2/subjects/DTI
cd /media/lmr2/subjects/DTI
/usr/local/freesurfer/bin/bbregister --s 4_FS --init-fsl --dti --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2anatorig.bbr.mat
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
mri_convert /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii...
crypt_gkey = FS8AfEXkNgFJk
fslregister --s 4_FS --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister --dof 6 --fsvol brainmask.mgz
Log file is /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat.fslregister.log
lø. 02. juli 09:52:39 +0200 2016
--s 4_FS --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
dmed4870
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/media/lmr2/subjects/DTI
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/refvol.fslregister.nii
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz...
crypt_gkey = FS8AfEXkNgFJk
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, 6.33299e-08, 5.7742e-08)
j_ras = (-4.84288e-08, 5.82077e-10, -1)
k_ras = (-1.49012e-08, 1, -4.65661e-10)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/refvol.fslregister.nii...
crypt_gkey = FS8AfEXkNgFJk
--------------------------------------
/media/lmr2/subjects/DTI
mri_convert /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii --frame 0
mri_convert /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii...
crypt_gkey = FS8AfEXkNgFJk
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 0
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii...
crypt_gkey = FS8AfEXkNgFJk
Mov determinant is -15.625
/media/lmr2/subjects/DTI
tkregister2_cmdl --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/reg0.2689.dat --regheader --fslregout /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat.fsl.mat0 --s 4_FS --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii
reg file /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/reg0.2689.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /media/lmr2/subjects/DTI/4_FS/mri/orig.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.500 0.000 0.000 120.000;
0.000 0.000 2.500 -75.000;
0.000 -2.500 0.000 120.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.000 -0.000 0.000 -0.597;
-0.000 -0.000 1.000 -19.206;
0.000 -1.000 0.000 10.283;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.000 0.000 -0.597;
-0.000 -0.000 1.000 -19.206;
0.000 -1.000 0.000 10.283;
0.000 0.000 0.000 1.000;
Determinant 1
subject = 4_FS
RegMat ---------------------------
1.000 -0.000 0.000 -0.597;
-0.000 -0.000 1.000 -19.206;
0.000 -1.000 0.000 10.283;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -15.625, ref det = -1
lø. 02. juli 09:52:44 +0200 2016
/media/lmr2/subjects/DTI
flirt.fsl -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/refvol.fslregister.nii -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat.fsl.mat0
lø. 02. juli 09:52:53 +0200 2016
/media/lmr2/subjects/DTI
flirt.fsl -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/refvol.fslregister.nii -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat.fsl.mat -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s 4_FS --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --fslreg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
1.000 0.007 -0.008 7.405;
-0.008 0.047 -0.999 181.317;
-0.007 0.999 0.047 15.278;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
reg file /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /media/lmr2/subjects/DTI/4_FS/mri/orig.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
Tmov: --------------------
-2.500 0.000 0.000 120.000;
0.000 0.000 2.500 -75.000;
0.000 -2.500 0.000 120.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -15.625, ref det = -1
---- Input registration matrix (computed) --------
1.000 0.007 -0.008 -0.263;
0.008 0.047 0.999 -17.435;
0.007 -0.999 0.047 9.025;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.007 -0.008 -0.263;
0.008 0.047 0.999 -17.435;
0.007 -0.999 0.047 9.025;
0.000 0.000 0.000 1.000;
Determinant 1
subject = 4_FS
RegMat ---------------------------
1.000 0.007 -0.008 -0.263;
0.008 0.047 0.999 -17.435;
0.007 -0.999 0.047 9.025;
0.000 0.000 0.000 1.000;
(standard_in) 1: illegal character: _
(standard_in) 1: syntax error
(standard_in) 1: illegal character: S
Started at lø. 02. juli 09:52:39 +0200 2016
Ended at lø. 02. juli 09:53:08 +0200 2016
fslregister Done
To check results, run:
tkregister2 --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --surf orig
mri_segreg --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --init-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --out-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/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 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /media/lmr2/subjects/DTI
cd /media/lmr2/subjects/DTI
mri_segreg --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --init-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat --out-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/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 dmed4870
machine x86_64
user lmr
movvol /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
regfile /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.init.dat
subject 4_FS
dof 6
outregfile /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/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 1467851012
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 0.007 -0.008 -0.263;
0.008 0.047 0.999 -17.435;
0.007 -0.999 0.047 9.025;
0.000 0.000 0.000 1.000;
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
Projecting RH Surfs
Computing relative cost
0 -25.0 -25.0 -25.0 1.000294
1 -25.0 -25.0 25.0 0.988980
2 -25.0 25.0 -25.0 1.036118
3 -25.0 25.0 25.0 1.031183
4 25.0 -25.0 -25.0 0.985025
5 25.0 -25.0 25.0 0.996169
6 25.0 25.0 -25.0 1.022202
7 25.0 25.0 25.0 1.019293
REL: 8 0.453350 8.079264 1.009908 rel = 0.448903
Initial costs ----------------
Number of surface hits 2626
WM Intensity 69.5511 +/- 24.9085
Ctx Intensity 85.9432 +/- 34.4600
Pct Contrast 19.0840 +/- 28.8318
Cost 0.4534
RelCost 0.4489
------------------------------------
Brute force preopt -4 4 4, n = 729
0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9678 0.9678 0.0
1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9166 0.9166 0.0
6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8458 0.8458 0.0
15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8198 0.8198 0.0
21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8127 0.8127 0.0
30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7870 0.7870 0.0
33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.7155 0.7155 0.0
273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.6575 0.6575 0.0
274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.4026 0.4026 0.0
Brute Force --------------------------
Min cost was 0.402645
Number of iterations 729
Search time 1.478000 sec
Parameters at best (transmm, rotdeg)
0.000 -4.000 0.000 -4.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 -4
2 0
3 -4
4 0
5 0
11 -0.002 -4.000 0.000 -4.000 0.000 0.000 0.4026446635
14 -0.002 -3.000 0.000 -4.000 0.000 0.000 0.3493283460
19 -0.002 -2.925 0.000 -4.000 0.000 0.000 0.3452824230
21 -0.002 -2.867 0.000 -4.000 0.000 0.000 0.3443744935
22 -0.002 -2.869 0.000 -4.000 0.000 0.000 0.3443717726
23 -0.002 -2.871 0.000 -4.000 0.000 0.000 0.3443707392
26 -0.002 -2.870 0.000 -4.000 0.000 0.000 0.3443701229
28 -0.002 -2.870 1.000 -4.000 0.000 0.000 0.3031553779
34 -0.002 -2.870 1.003 -4.000 0.000 0.000 0.3031543619
38 -0.002 -2.870 1.003 -3.000 0.000 0.000 0.2685454455
42 -0.002 -2.870 1.003 -3.382 0.000 0.000 0.2669712192
46 -0.002 -2.870 1.003 -3.356 0.000 0.000 0.2667957867
47 -0.002 -2.870 1.003 -3.347 0.000 0.000 0.2667738607
48 -0.002 -2.870 1.003 -3.342 0.000 0.000 0.2667703708
49 -0.002 -2.870 1.003 -3.343 0.000 0.000 0.2667699439
56 -0.002 -2.870 1.003 -3.343 0.382 0.000 0.2653949924
57 -0.002 -2.870 1.003 -3.343 0.216 0.000 0.2594442510
58 -0.002 -2.870 1.003 -3.343 0.201 0.000 0.2590204253
60 -0.002 -2.870 1.003 -3.343 0.179 0.000 0.2587689965
67 -0.002 -2.870 1.003 -3.343 0.179 -0.618 0.2523201769
69 -0.002 -2.870 1.003 -3.343 0.179 -0.446 0.2491039009
71 -0.002 -2.870 1.003 -3.343 0.179 -0.480 0.2490607082
72 -0.002 -2.870 1.003 -3.343 0.179 -0.465 0.2490274747
73 -0.002 -2.870 1.003 -3.343 0.179 -0.466 0.2490272548
83 -0.009 -2.870 1.003 -3.343 0.179 -0.466 0.2489727055
84 -0.021 -2.870 1.003 -3.343 0.179 -0.466 0.2489156312
86 -0.024 -2.870 1.003 -3.343 0.179 -0.466 0.2489119882
87 -0.025 -2.870 1.003 -3.343 0.179 -0.466 0.2489117500
90 -0.025 -1.870 1.003 -3.343 0.179 -0.466 0.2376213307
94 -0.025 -2.252 1.003 -3.343 0.179 -0.466 0.2314650665
99 -0.025 -2.277 1.003 -3.343 0.179 -0.466 0.2311997605
100 -0.025 -2.281 1.003 -3.343 0.179 -0.466 0.2311921795
107 -0.025 -2.281 0.385 -3.343 0.179 -0.466 0.2287382288
109 -0.025 -2.281 0.665 -3.343 0.179 -0.466 0.2262746734
110 -0.025 -2.281 0.641 -3.343 0.179 -0.466 0.2262076486
112 -0.025 -2.281 0.643 -3.343 0.179 -0.466 0.2262075540
115 -0.025 -2.281 0.643 -2.343 0.179 -0.466 0.2031611371
119 -0.025 -2.281 0.643 -2.725 0.179 -0.466 0.2010605446
120 -0.025 -2.281 0.643 -2.569 0.179 -0.466 0.1996154922
123 -0.025 -2.281 0.643 -2.536 0.179 -0.466 0.1994218206
124 -0.025 -2.281 0.643 -2.516 0.179 -0.466 0.1993678850
126 -0.025 -2.281 0.643 -2.521 0.179 -0.466 0.1993626171
127 -0.025 -2.281 0.643 -2.520 0.179 -0.466 0.1993626051
137 -0.025 -2.281 0.643 -2.520 0.228 -0.466 0.1989002635
138 -0.025 -2.281 0.643 -2.520 0.224 -0.466 0.1988923941
139 -0.025 -2.281 0.643 -2.520 0.222 -0.466 0.1988904245
148 -0.025 -2.281 0.643 -2.520 0.222 -0.479 0.1988140505
150 -0.025 -2.281 0.643 -2.520 0.222 -0.522 0.1987014730
162 -0.004 -2.281 0.643 -2.520 0.222 -0.522 0.1985730950
163 -0.002 -2.281 0.643 -2.520 0.222 -0.522 0.1985728080
170 -0.002 -1.899 0.643 -2.520 0.222 -0.522 0.1962360576
171 -0.002 -2.047 0.643 -2.520 0.222 -0.522 0.1944260999
172 -0.002 -2.051 0.643 -2.520 0.222 -0.522 0.1944010179
174 -0.002 -2.065 0.643 -2.520 0.222 -0.522 0.1943671405
175 -0.002 -2.063 0.643 -2.520 0.222 -0.522 0.1943655863
184 -0.002 -2.063 0.374 -2.520 0.222 -0.522 0.1895133973
185 -0.002 -2.063 0.365 -2.520 0.222 -0.522 0.1894760821
188 -0.002 -2.063 0.362 -2.520 0.222 -0.522 0.1894714564
189 -0.002 -2.063 0.361 -2.520 0.222 -0.522 0.1894712131
190 -0.002 -2.063 0.360 -2.520 0.222 -0.522 0.1894711812
200 -0.002 -2.063 0.360 -2.666 0.222 -0.522 0.1892134373
202 -0.002 -2.063 0.360 -2.610 0.222 -0.522 0.1888998485
206 -0.002 -2.063 0.360 -2.616 0.222 -0.522 0.1888993445
215 -0.002 -2.063 0.360 -2.616 0.236 -0.522 0.1887766160
216 -0.002 -2.063 0.360 -2.616 0.265 -0.522 0.1887018599
217 -0.002 -2.063 0.360 -2.616 0.260 -0.522 0.1886937541
226 -0.002 -2.063 0.360 -2.616 0.260 -0.439 0.1883765539
227 -0.002 -2.063 0.360 -2.616 0.260 -0.447 0.1883218594
228 -0.002 -2.063 0.360 -2.616 0.260 -0.467 0.1882879503
230 -0.002 -2.063 0.360 -2.616 0.260 -0.464 0.1882869811
241 -0.121 -2.063 0.360 -2.616 0.260 -0.464 0.1868178045
242 -0.127 -2.063 0.360 -2.616 0.260 -0.464 0.1867793331
245 -0.144 -2.063 0.360 -2.616 0.260 -0.464 0.1867196446
246 -0.147 -2.063 0.360 -2.616 0.260 -0.464 0.1867165992
248 -0.148 -2.063 0.360 -2.616 0.260 -0.464 0.1867162002
255 -0.148 -2.075 0.360 -2.616 0.260 -0.464 0.1866075497
257 -0.148 -2.103 0.360 -2.616 0.260 -0.464 0.1865245355
258 -0.148 -2.100 0.360 -2.616 0.260 -0.464 0.1865137232
259 -0.148 -2.095 0.360 -2.616 0.260 -0.464 0.1865107557
260 -0.148 -2.097 0.360 -2.616 0.260 -0.464 0.1865104854
268 -0.148 -2.097 0.317 -2.616 0.260 -0.464 0.1864249180
269 -0.148 -2.097 0.325 -2.616 0.260 -0.464 0.1864158247
270 -0.148 -2.097 0.327 -2.616 0.260 -0.464 0.1864146525
271 -0.148 -2.097 0.331 -2.616 0.260 -0.464 0.1864137404
282 -0.148 -2.097 0.331 -2.614 0.260 -0.464 0.1863786137
283 -0.148 -2.097 0.331 -2.583 0.260 -0.464 0.1861022673
293 -0.148 -2.097 0.331 -2.583 0.290 -0.464 0.1858754480
294 -0.148 -2.097 0.331 -2.583 0.306 -0.464 0.1858715975
295 -0.148 -2.097 0.331 -2.583 0.299 -0.464 0.1858620939
297 -0.148 -2.097 0.331 -2.583 0.300 -0.464 0.1858620277
308 -0.148 -2.097 0.331 -2.583 0.300 -0.456 0.1858511797
320 -0.178 -2.097 0.331 -2.583 0.300 -0.456 0.1858447302
321 -0.164 -2.097 0.331 -2.583 0.300 -0.456 0.1857992982
332 -0.164 -2.094 0.331 -2.583 0.300 -0.456 0.1857970052
333 -0.164 -2.093 0.331 -2.583 0.300 -0.456 0.1857969709
342 -0.164 -2.093 0.322 -2.583 0.300 -0.456 0.1857759727
343 -0.164 -2.093 0.318 -2.583 0.300 -0.456 0.1857728180
344 -0.164 -2.093 0.317 -2.583 0.300 -0.456 0.1857727020
355 -0.164 -2.093 0.317 -2.580 0.300 -0.456 0.1857702090
364 -0.164 -2.093 0.317 -2.580 0.308 -0.456 0.1857675137
365 -0.164 -2.093 0.317 -2.580 0.305 -0.456 0.1857649522
366 -0.164 -2.093 0.317 -2.580 0.304 -0.456 0.1857645966
376 -0.164 -2.093 0.317 -2.580 0.304 -0.460 0.1857623370
388 -0.161 -2.093 0.317 -2.580 0.304 -0.460 0.1857613212
409 -0.161 -2.093 0.316 -2.580 0.304 -0.460 0.1857609657
410 -0.161 -2.093 0.315 -2.580 0.304 -0.460 0.1857609308
422 -0.161 -2.093 0.315 -2.583 0.304 -0.460 0.1857605290
424 -0.161 -2.093 0.315 -2.582 0.304 -0.460 0.1857601436
434 -0.161 -2.093 0.315 -2.582 0.303 -0.460 0.1857594968
444 -0.161 -2.093 0.315 -2.582 0.303 -0.462 0.1857590269
Powell done niters = 5
Computing relative cost
0 -25.0 -25.0 -25.0 1.005334
1 -25.0 -25.0 25.0 1.000954
2 -25.0 25.0 -25.0 1.001147
3 -25.0 25.0 25.0 1.040963
4 25.0 -25.0 -25.0 1.003520
5 25.0 -25.0 25.0 0.998242
6 25.0 25.0 -25.0 1.027747
7 25.0 25.0 25.0 1.004927
REL: 8 0.185759 8.082833 1.010354 rel = 0.183855
Number of iterations 5
Min cost was 0.185759
Number of FunctionCalls 447
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.909000 sec
Parameters at optimum (transmm) -0.16139 -2.09326 0.31456
Parameters at optimum (rotdeg) -2.58184 0.30296 -0.46166
Final costs ----------------
Number of surface hits 2626
WM Intensity 62.8003 +/- 19.8330
Ctx Intensity 83.8183 +/- 27.7584
Pct Contrast 27.3649 +/- 22.2036
Cost 0.1858
RelCost 0.4489
Reg at min cost was
1.000 0.001 -0.000 -0.509;
0.000 0.002 1.000 -19.102;
0.001 -1.000 0.002 10.117;
0.000 0.000 0.000 1.000;
Writing optimal reg to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/bbr.pass1.dat, type = 14
Original Reg
1.000 0.007 -0.008 -0.263;
0.008 0.047 0.999 -17.435;
0.007 -0.999 0.047 9.025;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
-0.000 0.005 -0.008 0.247;
0.008 0.045 -0.001 1.667;
0.006 0.001 0.045 -1.092;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 2.113631
Computing change in rh position
Surface RMS Diff (mm) 2.237073 5.464361
mri_segreg done
mri_segreg --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --init-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/bbr.pass1.dat --out-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /media/lmr2/subjects/DTI
cd /media/lmr2/subjects/DTI
mri_segreg --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii --init-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/bbr.pass1.dat --out-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
sysname Linux
hostname dmed4870
machine x86_64
user lmr
movvol /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/template.nii
regfile /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/tmp.bbregister.2620/bbr.pass1.dat
subject 4_FS
dof 6
outregfile /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/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 1468277285
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 0.001 -0.000 -0.509;
0.000 0.002 1.000 -19.102;
0.001 -1.000 0.002 10.117;
0.000 0.000 0.000 1.000;
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
Projecting RH Surfs
Computing relative cost
0 -25.0 -25.0 -25.0 1.008927
1 -25.0 -25.0 25.0 0.996429
2 -25.0 25.0 -25.0 0.998244
3 -25.0 25.0 25.0 1.011046
4 25.0 -25.0 -25.0 1.006111
5 25.0 -25.0 25.0 1.022131
6 25.0 25.0 -25.0 1.006253
7 25.0 25.0 25.0 1.019412
REL: 8 0.184957 8.068553 1.008569 rel = 0.183386
Initial costs ----------------
Number of surface hits 262301
WM Intensity 63.0659 +/- 20.2330
Ctx Intensity 84.3542 +/- 27.6460
Pct Contrast 27.7983 +/- 22.4531
Cost 0.1850
RelCost 0.1834
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1941 0.1941 0.0
1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1935 0.1935 0.0
3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1915 0.1915 0.0
30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1890 0.1890 0.0
31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1888 0.1888 0.0
40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1885 0.1885 0.0
111 -0.1000 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.1881 0.1881 0.0
112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1881 0.1881 0.0
121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1881 0.1881 0.0
212 -0.1000 0.1000 0.0000 0.1000 0.0000 0.1000 0.1877 0.1877 0.0
337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1876 0.1876 0.0
354 0.0000 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.1867 0.1867 0.0
355 0.0000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1866 0.1866 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1858 0.1858 0.0
482 0.0000 0.1000 0.1000 0.1000 0.0000 0.1000 0.1857 0.1857 0.0
Brute Force --------------------------
Min cost was 0.185736
Number of iterations 729
Search time 1.433000 sec
Parameters at best (transmm, rotdeg)
0.000 0.100 0.100 0.100 0.000 0.100
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0.1
2 0.1
3 0.1
4 0
5 0.1
7 -0.036 0.100 0.100 0.100 0.000 0.100 0.1846664188
8 -0.065 0.100 0.100 0.100 0.000 0.100 0.1846556675
9 -0.052 0.100 0.100 0.100 0.000 0.100 0.1846421578
18 -0.052 0.069 0.100 0.100 0.000 0.100 0.1845751865
20 -0.052 0.068 0.100 0.100 0.000 0.100 0.1845751658
28 -0.052 0.068 0.054 0.100 0.000 0.100 0.1844988156
29 -0.052 0.068 0.062 0.100 0.000 0.100 0.1844944182
30 -0.052 0.068 0.063 0.100 0.000 0.100 0.1844943872
39 -0.052 0.068 0.063 0.098 0.000 0.100 0.1844940572
49 -0.052 0.068 0.063 0.098 0.025 0.100 0.1844455415
51 -0.052 0.068 0.063 0.098 0.023 0.100 0.1844451603
60 -0.052 0.068 0.063 0.098 0.023 -0.043 0.1834523116
61 -0.052 0.068 0.063 0.098 0.023 -0.048 0.1834449712
62 -0.052 0.068 0.063 0.098 0.023 -0.065 0.1834299176
65 -0.052 0.068 0.063 0.098 0.023 -0.068 0.1834295496
75 -0.087 0.068 0.063 0.098 0.023 -0.068 0.1832867211
76 -0.096 0.068 0.063 0.098 0.023 -0.068 0.1832746778
77 -0.103 0.068 0.063 0.098 0.023 -0.068 0.1832721656
78 -0.102 0.068 0.063 0.098 0.023 -0.068 0.1832720510
86 -0.102 0.067 0.063 0.098 0.023 -0.068 0.1832710554
87 -0.102 0.060 0.063 0.098 0.023 -0.068 0.1832686244
89 -0.102 0.061 0.063 0.098 0.023 -0.068 0.1832686148
97 -0.102 0.061 0.059 0.098 0.023 -0.068 0.1832677969
98 -0.102 0.061 0.060 0.098 0.023 -0.068 0.1832677510
115 -0.102 0.061 0.060 0.098 0.088 -0.068 0.1832613167
116 -0.102 0.061 0.060 0.098 0.056 -0.068 0.1831776112
117 -0.102 0.061 0.060 0.098 0.055 -0.068 0.1831775236
126 -0.102 0.061 0.060 0.098 0.055 -0.075 0.1831740346
127 -0.102 0.061 0.060 0.098 0.055 -0.079 0.1831733784
129 -0.102 0.061 0.060 0.098 0.055 -0.078 0.1831733675
139 -0.107 0.061 0.060 0.098 0.055 -0.078 0.1831712169
149 -0.107 0.058 0.060 0.098 0.055 -0.078 0.1831707176
150 -0.107 0.059 0.060 0.098 0.055 -0.078 0.1831706331
160 -0.107 0.059 0.061 0.098 0.055 -0.078 0.1831706151
178 -0.107 0.059 0.061 0.098 0.059 -0.078 0.1831695384
224 -0.107 0.059 0.061 0.099 0.058 -0.078 0.1831694619
249 -0.107 0.059 0.061 0.099 0.058 -0.079 0.1831694346
271 -0.107 0.060 0.061 0.099 0.058 -0.080 0.1831694308
310 -0.107 0.060 0.061 0.099 0.058 -0.079 0.1831694308
311 -0.107 0.060 0.061 0.099 0.058 -0.078 0.1831694156
320 -0.108 0.060 0.061 0.099 0.058 -0.078 0.1831694088
Powell done niters = 5
Computing relative cost
0 -25.0 -25.0 -25.0 1.008320
1 -25.0 -25.0 25.0 0.995446
2 -25.0 25.0 -25.0 0.998005
3 -25.0 25.0 25.0 1.011432
4 25.0 -25.0 -25.0 1.006726
5 25.0 -25.0 25.0 1.020961
6 25.0 25.0 -25.0 1.006024
7 25.0 25.0 25.0 1.017753
REL: 8 0.183169 8.064668 1.008084 rel = 0.181701
Number of iterations 5
Min cost was 0.183169
Number of FunctionCalls 372
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 45.611000 sec
Parameters at optimum (transmm) -0.10840 0.05969 0.06080
Parameters at optimum (rotdeg) 0.09873 0.05816 -0.07842
Final costs ----------------
Number of surface hits 262301
WM Intensity 63.0614 +/- 20.1933
Ctx Intensity 84.4511 +/- 27.6328
Pct Contrast 27.9266 +/- 22.4239
Cost 0.1832
RelCost 0.1834
Reg at min cost was
1.000 0.000 0.001 -0.634;
-0.001 0.003 1.000 -19.059;
0.000 -1.000 0.003 10.146;
0.000 0.000 0.000 1.000;
Writing optimal reg to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat, type = 14
Original Reg
1.000 0.001 -0.000 -0.509;
0.000 0.002 1.000 -19.102;
0.001 -1.000 0.002 10.117;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
-0.000 0.001 -0.001 0.124;
0.001 -0.002 0.000 -0.043;
0.001 -0.000 -0.002 -0.028;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 0.166697
Computing change in rh position
Surface RMS Diff (mm) 0.149591 0.288353
mri_segreg done
tkregister2_cmdl --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/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 /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz
reg file /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
1.000 0.000 0.001 -0.634;
-0.001 0.003 1.000 -19.059;
0.000 -1.000 0.003 10.146;
0.000 0.000 0.000 1.000;
float2int = 0
---------------------------------------
INFO: loading target /media/lmr2/subjects/DTI/4_FS/mri/orig.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz
Tmov: --------------------
-2.500 0.000 0.000 120.000;
0.000 0.000 2.500 -75.000;
0.000 -2.500 0.000 120.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
1.000 0.000 0.001 -0.634;
-0.001 0.003 1.000 -19.059;
0.000 -1.000 0.003 10.146;
0.000 0.000 0.000 1.000;
Determinant 1
subject = 4_FS
RegMat ---------------------------
1.000 0.000 0.001 -0.634;
-0.001 0.003 1.000 -19.059;
0.000 -1.000 0.003 10.146;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -15.625, ref det = -1
Cleaning up
Started at lø. 02. juli 09:52:32 +0200 2016
Ended at lø. 02. juli 09:54:24 +0200 2016
BBR-Run-Time-Sec 112
bbregister Done
To check results, run:
tkregister2 --mov /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz --reg /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.dat --surf
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -concat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2diff.bbr.mat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2anat.bbr.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration lø. 02. juli 09:54:25 +0200 2016
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_mni.nii.gz -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/mni2anat.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2mni.bbr.mat -concat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/mni2diff.bbr.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2mni.mat -concat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/mni2anatorig.mat -inverse /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks lø. 02. juli 09:57:16 +0200 2016
mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter.nii.gz
Binarizing based on matching values
nMatch 5
0 2
1 7
2 41
3 46
4 77
binval 1
binvalnot 0
Found 470670 values in range
Counting number of voxels
Found 470670 voxels in final mask
mri_binarize done
mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter++.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter++.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter++.nii.gz
Binarizing based on matching values
nMatch 8
0 2
1 7
2 41
3 46
4 77
5 28
6 60
7 16
binval 1
binvalnot 0
Found 501971 values in range
Counting number of voxels
Found 501971 voxels in final mask
mri_binarize done
mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
0 4
1 43
binval 0
binvalnot 1
Found 5201 values in range
Counting number of voxels
Found 5201 voxels in final mask
mri_binarize done
mri_aparc2aseg --s 4_FS --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /media/lmr2/subjects/DTI
subject 4_FS
outvol /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/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
/media/lmr2/subjects/DTI/4_FS/surf/lh.white
Reading lh pial surface
/media/lmr2/subjects/DTI/4_FS/surf/lh.pial
Loading lh annotations from /media/lmr2/subjects/DTI/4_FS/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
/media/lmr2/subjects/DTI/4_FS/surf/rh.white
Reading rh pial surface
/media/lmr2/subjects/DTI/4_FS/surf/rh.pial
Loading rh annotations from /media/lmr2/subjects/DTI/4_FS/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 /media/lmr2/subjects/DTI/4_FS/mri/ribbon.mgz
Loading filled from /media/lmr2/subjects/DTI/4_FS/mri/filled.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /media/lmr2/subjects/DTI/4_FS/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
-------------------------
Labeling Slice
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 919909
Used brute-force search on 0 voxels
Fixing Parahip LH WM
Found 8 clusters
0 k 1.000000
1 k 1.000000
2 k 4.000000
3 k 1.000000
4 k 1.000000
5 k 1.000000
6 k 983.000000
7 k 1.000000
Fixing Parahip RH WM
Found 2 clusters
0 k 1.000000
1 k 1022.000000
Writing output aseg to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min 1000
max 2999
binval 1
binvalnot 0
Found 482341 values in range
Counting number of voxels
Found 482341 voxels in final mask
mri_binarize done
mri_binarize --i /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min 1000
max 4999
binval 1
binvalnot 0
Found 760015 values in range
Counting number of voxels
Found 760015 voxels in final mask
mri_binarize done
mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 16 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/Brain-Stem.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/lmr2/subjects/DTI
cmdline mri_binarize --i /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz --match 16 --o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/Brain-Stem.nii.gz
sysname Linux
hostname dmed4870
machine x86_64
user lmr
input /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
0 16
binval 1
binvalnot 0
Found 22574 values in range
Counting number of voxels
Found 22574 voxels in final mask
mri_binarize done
fslmaths /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz -add /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/Brain-Stem.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/4_FS/mri/brainmask.mgz...
crypt_gkey = FS8AfEXkNgFJk
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, 6.33299e-08, 5.7742e-08)
j_ras = (-4.84288e-08, 5.82077e-10, -1)
k_ras = (-1.49012e-08, 1, -4.65661e-10)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
fslmaths /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /media/lmr2/subjects/DTI/4_FS/mri/aparc+aseg.mgz...
crypt_gkey = FS8AfEXkNgFJk
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, 6.33299e-08, 5.7742e-08)
j_ras = (-4.84288e-08, 5.82077e-10, -1)
k_ras = (-1.49012e-08, 1, -4.65661e-10)
writing to /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz...
crypt_gkey = FS8AfEXkNgFJk
fslmaths /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter++.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter++.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter++.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter++.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/notventricles.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/notventricles.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/notventricles.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/notventricles.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/cortex.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm+bs.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm+bs.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg+2mm.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg+2mm.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg_mask.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg_mask.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask-vent.nii.gz
fslorient -forceradiological /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask-vent.nii.gz
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/lowb.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz -k /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi_snr.txt
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/brain_anat_orig.nii.gz -out /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit lø. 02. juli 10:02:28 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016_nativerows/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at lø. 02. juli 10:02:29 +0200 2016
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