Hi Anastasia
Thanks. I am sending my entire trac-all.log
Knut Jøgen
On 07/12/2016 11:19 PM, Anastasia Yendiki wrote:
Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks!
a.y
On Mon, 11 Jul 2016, Knut J Bjuland wrote:
flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat
-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
terminate called after throwing an instance of
'NEWMAT::SingularException'
Abort (core dumped)
ERROR: flirt
Fedora 24
glibc-2.23.1-8.fc24.x86_64
gcc-6.1.1-3.fc24.x86_64
libstdc++-6.1.1-3.fc24.x86_64
ldd /usr/local/freesurfer/bin/flirt.fsl
linux-vdso.so.1 (0x00007ffe8b6c8000)
libz.so.1 => /lib64/libz.so.1 (0x00007feaeba06000)
libstdc++.so.6 => /lib64/libstdc++.so.6
(0x00007feaeb67e000)
libm.so.6 => /lib64/libm.so.6 (0x00007feaeb374000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007feaeb15d000)
libc.so.6 => /lib64/libc.so.6 (0x00007feaead9a000)
/lib64/ld-linux-x86-64.so.2 (0x0000557ba6f46000)
Knut Jørgen Bjuland
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Wed Jul 13 16:32:42 CEST 2016
/home/knutjbj/subjects
/usr/local/freesurfer/bin/trac-all
-prep -c dmric.4_test
Subject 4_test
SUBJECTS_DIR /home/knutjbj/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer60
build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160706-3f44648
knutjbj
loalhost
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 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 127405
maxlocks unlimited
maxsignal 127405
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32845380 9620068 16527136 169380 6698176 22482108
Swap: 71678968 0 71678968
########################################
Program versions:
$Id: trac-all,v 1.60 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.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: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/13-14:32:42-GMT BuildTimeStamp: Jul 6 2016 17:01:27 CVS: User: knutjbj Machine: loalhost Platform: Linux PlatformVersion: 4.6.3-300.fc24.x86_64 CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
knutjbj
loalhost
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 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 127405
maxlocks unlimited
maxsignal 127405
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32845380 9620980 16526224 169380 6698176 22481488
Swap: 71678968 0 71678968
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Jul 13 16:32:42 CEST 2016
mri_convert /home/knutjbj/subjects/sMRIdata/rawdata/4_test/dti/DTIDKI.nii.gz /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz
mri_convert.bin /home/knutjbj/subjects/sMRIdata/rawdata/4_test/dti/DTIDKI.nii.gz /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/sMRIdata/rawdata/4_test/dti/DTIDKI.nii.gz...
TR=8800.00, 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 /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz...
cp /home/knutjbj/subjects/sMRIdata/rawdata/4_test/dti/DTIDKI_row_3_m_-1.bvec /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvecs
cp /home/knutjbj/subjects/sMRIdata/rawdata/4_test/dti/DTIDKI.bval /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvals
mv -f /home/knutjbj/subjects/4_test/dmri/bvecs.tmp /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvecs
mv -f /home/knutjbj/subjects/4_test/dmri/bvals.tmp /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvals
flip4fsl /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -15.625
fslswapdim /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz x y z /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.nii.gz
INFO: found /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /home/knutjbj/subjects/4_test/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.mghdti.bvecs /home/knutjbj/subjects/4_test/dmri/bvecs
mv -f /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.mghdti.bvals /home/knutjbj/subjects/4_test/dmri/bvals
eddy_correct /home/knutjbj/subjects/4_test/dmri/dwi_orig_flip.nii.gz /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz 0
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0000
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0001
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0002
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0003
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0004
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0005
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0006
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0007
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0008
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0009
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0010
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0011
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0012
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0013
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0014
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0015
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0016
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0017
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0018
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0019
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0020
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0021
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0022
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0023
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0024
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0025
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0026
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0027
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0028
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0029
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0030
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0031
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0032
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0033
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0034
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0035
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0036
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0037
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0038
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0039
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0040
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0041
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0042
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0043
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0044
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0045
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0046
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0047
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0048
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0049
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0050
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0051
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0052
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0053
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0054
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0055
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0056
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0057
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0058
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0059
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0060
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0061
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0062
processing /home/knutjbj/subjects/4_test/dmri/dwi_tmp0063
mv -f /home/knutjbj/subjects/4_test/dmri/bvecs /home/knutjbj/subjects/4_test/dmri/bvecs.norot
xfmrot /home/knutjbj/subjects/4_test/dmri/dwi.ecclog /home/knutjbj/subjects/4_test/dmri/bvecs.norot /home/knutjbj/subjects/4_test/dmri/bvecs
ln -sf /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz /home/knutjbj/subjects/4_test/dmri/data.nii.gz
mri_convert --frame 0 61 62 63 /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz
mri_convert.bin --frame 0 61 62 63 /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 0 61 62 63
writing to /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz...
mri_concat --i /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz --mean --o /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Computing mean across frames
Writing to /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz
bet /home/knutjbj/subjects/4_test/dmri/lowb.nii.gz /home/knutjbj/subjects/4_test/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/knutjbj/subjects/4_test/dmri/lowb_brain_mask.nii.gz /home/knutjbj/subjects/4_test/dlabel/diff
#-------------------------------------
#@# Image quality assessment Wed Jul 13 16:37:16 CEST 2016
/usr/local/freesurfer/bin/dmri_motion --dwi /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz --mat /home/knutjbj/subjects/4_test/dmri/dwi.ecclog --bval /home/knutjbj/subjects/4_test/dmri/bvals --T 39.168922 --out /home/knutjbj/subjects/4_test/dmri/dwi_motion.txt
cwd /home/knutjbj/subjects
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz --mat /home/knutjbj/subjects/4_test/dmri/dwi.ecclog --bval /home/knutjbj/subjects/4_test/dmri/bvals --T 39.168922 --out /home/knutjbj/subjects/4_test/dmri/dwi_motion.txt
sysname Linux
hostname loalhost
machine x86_64
user knutjbj
Output motion measure file: /home/knutjbj/subjects/4_test/dmri/dwi_motion.txt
Input transform file: /home/knutjbj/subjects/4_test/dmri/dwi.ecclog
Input DWI file: /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz
Input b-value table: /home/knutjbj/subjects/4_test/dmri/bvals
Low-b image intensity threshold: 39.1689
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 /home/knutjbj/subjects/4_test/dmri/dwi_orig.nii.gz
Loading b-value table from /home/knutjbj/subjects/4_test/dmri/bvals
Computing within-volume head motion measures
Done in 3.458 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Wed Jul 13 16:37:20 CEST 2016
mri_convert /home/knutjbj/subjects/4_test/mri/brain.mgz /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz
mri_convert.bin /home/knutjbj/subjects/4_test/mri/brain.mgz /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/4_test/mri/brain.mgz...
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, -7.45058e-09, 3.72529e-09)
j_ras = (0, 0, -1)
k_ras = (7.45058e-09, 1, -9.31323e-10)
writing to /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz...
flip4fsl /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz /home/knutjbj/subjects/4_test/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz x z -y /home/knutjbj/subjects/4_test/dmri/brain_anat.nii.gz
fslorient -forceradiological /home/knutjbj/subjects/4_test/dmri/brain_anat.nii.gz
tkregister2 --mov /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz --targ /home/knutjbj/subjects/4_test/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2anat.mat --reg /home/knutjbj/subjects/4_test/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target volume /home/knutjbj/subjects/4_test/dmri/brain_anat.nii.gz
movable volume /home/knutjbj/subjects/4_test/dmri/brain_anat_orig.nii.gz
reg file /home/knutjbj/subjects/4_test/dmri/xfms/anat2anatorig.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132 2016/05/04 22:17:15 greve Exp $
Diagnostic Level -1
INFO: loading target /home/knutjbj/subjects/4_test/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/knutjbj/subjects/4_test/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 0.00000;
-0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 1.00000;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
---- Input registration matrix --------
1.00000 -0.00000 0.00000 0.00000;
-0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 1.00000;
0.00000 0.00000 0.00000 1.00000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 -1.00000 0.00000;
0.00000 1.00000 0.00000 1.00000;
0.00000 0.00000 0.00000 1.00000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /home/knutjbj/subjects/4_test/dmri/xfms/anat2anatorig.mat -inverse /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2anat.mat
tmp /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658
Log file is /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat.log
Wed Jul 13 16:37:21 CEST 2016
setenv SUBJECTS_DIR /home/knutjbj/subjects
cd /home/knutjbj/subjects
/usr/local/freesurfer/bin/bbregister --s 4_test --init-fsl --dti --mov /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat /home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii
mri_convert.bin /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii...
fslregister --s 4_test --mov /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii --reg /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat --niters 1 --maxangle 90 --tmp /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
Log file is /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat.fslregister.log
Wed Jul 13 16:37:25 CEST 2016
--s 4_test --mov /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii --reg /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat --niters 1 --maxangle 90 --tmp /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
loalhost
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/knutjbj/subjects
mri_convert /home/knutjbj/subjects/4_test/mri/brainmask.mgz /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/refvol.fslregister.nii
mri_convert.bin /home/knutjbj/subjects/4_test/mri/brainmask.mgz /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/4_test/mri/brainmask.mgz...
TR=2300.00, TE=4.21, TI=996.00, flip angle=9.00
i_ras = (-1, -7.45058e-09, 3.72529e-09)
j_ras = (0, 0, -1)
k_ras = (7.45058e-09, 1, -9.31323e-10)
writing to /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/knutjbj/subjects
mri_convert /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii --frame 0
mri_convert.bin /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/template.nii...
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 /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii...
Mov determinant is -15.625
/home/knutjbj/subjects
tkregister2_cmdl --mov /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii --reg /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/reg0.13701.dat --regheader --fslregout /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat.fsl.mat0 --s 4_test --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii
reg file /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/reg0.13701.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132 2016/05/04 22:17:15 greve Exp $
Diagnostic Level -1
INFO: loading target /home/knutjbj/subjects/4_test/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/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.50000 0.00000 0.00000 120.00000;
0.00000 0.00000 2.50000 -75.00000;
0.00000 -2.50000 0.00000 120.00000;
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 -2.71777;
-0.00000 -0.00000 1.00000 -23.74727;
-0.00000 -1.00000 0.00000 7.36558;
0.00000 0.00000 0.00000 1.00000;
---------------------------------------
---- Input registration matrix --------
1.00000 0.00000 0.00000 -2.71777;
-0.00000 -0.00000 1.00000 -23.74727;
-0.00000 -1.00000 0.00000 7.36558;
0.00000 0.00000 0.00000 1.00000;
Determinant 1
subject = 4_test
RegMat ---------------------------
1.00000 0.00000 0.00000 -2.71777;
-0.00000 -0.00000 1.00000 -23.74727;
-0.00000 -1.00000 0.00000 7.36558;
0.00000 0.00000 0.00000 1.00000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -15.625, ref det = -1
Wed Jul 13 16:37:29 CEST 2016
/home/knutjbj/subjects
flirt.fsl -ref /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/refvol.fslregister.nii -in /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat.fsl.mat0
Wed Jul 13 16:37:36 CEST 2016
/home/knutjbj/subjects
flirt.fsl -ref /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/refvol.fslregister.nii -in /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/reg.init.dat.fsl.mat -init /home/knutjbj/subjects/4_test/dmri/xfms/tmp.bbregister.13658/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)
ERROR: flirt
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Jul 13 16:37:41 CEST 2016
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