Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for your
help.
Bahram
2015-08-17 19:31 GMT+02:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
>
> Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!
>
> a.y
>
>
> On Fri, 14 Aug 2015, B M wrote:
>
> Dear experts,
>> I have the last version of tTrakula. i did the first step with
>> trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> This worked properly to the end as shown below:
>> trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015
>>
>> However looking at logfile i found following errors:
>> flirt -in
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
>> -ref
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>> -applyxfm -init
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
>> -interp nearestneighbour
>> terminate called after throwing an instance of 'NEWMAT::SingularException'
>> Abort (core dumped)
>>
>> OR
>>
>> Loading brain mask of output subject from
>>
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> niiRead(): error opening file
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>> ERROR: Could not read
>> /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
>>
>>
>> AND as i tried the next step i got the following error:
>>
>> bm@bm-linux:~$ trac-all -bedp -c
>> bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
>> INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/
>> INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> WARN: Running FSL's bedbost locally - this might take a while
>> WARN: It is recommended to run this step on a cluster
>> bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
>> /usr/local/freesurfer/bin/bedpostx_mgh: 131:
>> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
>>
>> Could you please advise me what to do?
>> Best
>>
>> Bahram
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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>
Fri Aug 14 17:22:48 CEST 2015
/home/bm
/usr/local/freesurfer/bin/trac-all
-prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
Subject P01-a
SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
bm
bm-linux
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 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 256954
maxlocks unlimited
maxsignal 256954
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 32909372 30981556 1927816 0 776952 25756624
-/+ buffers/cache: 4447980 28461392
Swap: 124999676 9000 124990676
########################################
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: 2015/08/14-15:22:48-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
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: 2015/08/14-15:22:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
New invocation of trac-preproc
bm
bm-linux
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 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 256954
maxlocks unlimited
maxsignal 256954
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 32909372 30983696 1925676 0 776952 25756624
-/+ buffers/cache: 4450120 28459252
Swap: 124999676 9000 124990676
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Aug 14 17:22:48 CEST 2015
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files/77655480 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files/77655480 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files/77655480...
crypt_gkey = *CcpE8.V7ZUkk
Getting Series No
INFO: Found 1762 files in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files
INFO: Scanning for Series Number 28
Scanning Directory
INFO: found 475 files in series
INFO: loading series header info.
RunNo = 27
INFO: sorting.
INFO: (128 128 19), nframes = 25, ismosaic=0
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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files/77655480
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName Larosa^Anna
Date and time
StudyDate 20070802
StudyTime 104028.453000
SeriesTime 112605.593000
AcqTime 112440.982485
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_dti 12richtungen
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 86
InversionTime -1
RepetitionTime 2800
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 27
SeriesNo 28
ImageNo 1
NImageRows 128
NImageCols 128
NFrames 25
SliceArraylSize 19
IsMosaic 0
ImgPos 115.0000 105.5569 -107.1683
VolRes 1.7969 1.7969 6.5000
VolDim 128 128 19
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 -9.4431 -45.4183
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=2800.00, TE=86.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
mri_probedicom --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/files/77655480 > bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dcminfo.dat
cp bmdaten/Auswertung/ALS-Review/Trakula/P01-a/files/bvecs.txt bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvecs
cp bmdaten/Auswertung/ALS-Review/Trakula/P01-a/files/bvals.txt bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvals
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs.tmp bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvecs
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvals.tmp bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvals
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 20.9869
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz x -y z bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.nii.gz
INFO: found bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.mghdti.bvecs bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.mghdti.bvals bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvals
eddy_correct bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig_flip.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz 0
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0000
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0001
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0002
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0003
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0004
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0005
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0006
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0007
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0008
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0009
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0010
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0011
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0012
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0013
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0014
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0015
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0016
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0017
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0018
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0019
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0020
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0021
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0022
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0023
processing bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_tmp0024
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs.norot
xfmrot bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.ecclog bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs.norot bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs
ln -sf bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/data.nii.gz
mri_convert --frame 0 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
mri_convert --frame 0 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
mri_concat --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz --mean --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Computing mean across frames
Writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
bet bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb_brain_mask.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff
#-------------------------------------
#@# Image quality assessment Fri Aug 14 17:26:05 CEST 2015
/usr/local/freesurfer/bin/dmri_motion --dwi bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz --mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.ecclog --bval bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvals --out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_motion.txt
cwd /home/bm
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_orig.nii.gz --mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.ecclog --bval bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvals --out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_motion.txt
sysname Linux
hostname bm-linux
machine x86_64
user bm
Output motion measure file: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/dwi_motion.txt
Input transform file: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/dwi.ecclog
Input DWI file: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/dwi_orig.nii.gz
Input b-value table: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/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 25 volumes
Loading DWI volume series from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/dwi_orig.nii.gz
Loading b-value table from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/bvals
Computing within-volume head motion measures
Done in 0.332 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Fri Aug 14 17:26:06 CEST 2015
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brain.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brain.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brain.mgz...
crypt_gkey = *CcpE8.V7ZUkk
TR=15.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz
tkregister2 --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz --targ bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz --regheader --noedit --fslregout bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2anat.mat --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target volume bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz
movable volume bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz
reg file bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2anatorig.mat -inverse bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2anat.mat
Log file is bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat.log
Fri Aug 14 17:26:07 CEST 2015
setenv SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/
cd /home/bm
/usr/local/freesurfer/bin/bbregister --s P01-a --init-fsl --dti --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat --fslmat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/diff2anatorig.bbr.mat
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii...
crypt_gkey = *CcpE8.V7ZUkk
fslregister --s P01-a --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister --dof 6 --fsvol brainmask.mgz
Log file is bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat.fslregister.log
Fri Aug 14 17:26:07 CEST 2015
--s P01-a --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
bm-linux
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/bm
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/refvol.fslregister.nii
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz...
crypt_gkey = *CcpE8.V7ZUkk
TR=15.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/refvol.fslregister.nii...
crypt_gkey = *CcpE8.V7ZUkk
--------------------------------------
/home/bm
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii --frame 0
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii...
crypt_gkey = *CcpE8.V7ZUkk
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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii...
crypt_gkey = *CcpE8.V7ZUkk
Mov determinant is -20.9869
/home/bm
tkregister2_cmdl --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/reg0.27172.dat --regheader --fslregout bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat.fsl.mat0 --s P01-a --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii
reg file bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/reg0.27172.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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.797 0.000 0.000 115.000;
0.000 0.000 6.500 -61.750;
0.000 -1.797 0.000 115.000;
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 5.585;
0.000 0.000 1.000 43.513;
0.000 -1.000 0.000 -8.646;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 0.000 5.585;
0.000 0.000 1.000 43.513;
0.000 -1.000 0.000 -8.646;
0.000 0.000 0.000 1.000;
Determinant 1
subject = P01-a
RegMat ---------------------------
1.000 0.000 0.000 5.585;
0.000 0.000 1.000 43.513;
0.000 -1.000 0.000 -8.646;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -20.9869, ref det = -1
Fri Aug 14 17:26:09 CEST 2015
/home/bm
flirt.fsl -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/refvol.fslregister.nii -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat.fsl.mat0
Fri Aug 14 17:26:14 CEST 2015
/home/bm
flirt.fsl -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/refvol.fslregister.nii -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat.fsl.mat -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s P01-a --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --fslreg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
1.000 -0.006 -0.009 19.483;
-0.009 0.025 -1.000 230.874;
0.006 1.000 0.025 0.968;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
reg file bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
Tmov: --------------------
-1.797 0.000 0.000 115.000;
0.000 0.000 6.500 -61.750;
0.000 -1.797 0.000 115.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -20.9869, ref det = -1
---- Input registration matrix (computed) --------
1.000 -0.006 -0.009 4.733;
0.009 0.025 1.000 43.213;
-0.006 -1.000 0.025 -8.775;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.006 -0.009 4.733;
0.009 0.025 1.000 43.213;
-0.006 -1.000 0.025 -8.775;
0.000 0.000 0.000 1.000;
Determinant 1
subject = P01-a
RegMat ---------------------------
1.000 -0.006 -0.009 4.733;
0.009 0.025 1.000 43.213;
-0.006 -1.000 0.025 -8.775;
0.000 0.000 0.000 1.000;
(standard_in) 1: illegal character: P
Started at Fri Aug 14 17:26:07 CEST 2015
Ended at Fri Aug 14 17:26:28 CEST 2015
fslregister Done
To check results, run:
tkregister2 --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --surf orig
mri_segreg --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --init-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --out-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/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 bmdaten/Auswertung/ALS-Review/Trakula/
cd /home/bm
mri_segreg --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --init-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat --out-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/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 bm-linux
machine x86_64
user bm
movvol bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
regfile bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.init.dat
subject P01-a
dof 6
outregfile bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/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 1439620376
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 -0.006 -0.009 4.733;
0.009 0.025 1.000 43.213;
-0.006 -1.000 0.025 -8.775;
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 1.057198
1 -25.0 -25.0 25.0 1.096240
2 -25.0 25.0 -25.0 1.000210
3 -25.0 25.0 25.0 1.040083
4 25.0 -25.0 -25.0 1.060578
5 25.0 -25.0 25.0 1.025362
6 25.0 25.0 -25.0 1.023075
7 25.0 25.0 25.0 1.057643
REL: 8 0.750672 8.360390 1.045049 rel = 0.718313
Initial costs ----------------
Number of surface hits 2387
WM Intensity 242.5092 +/- 74.4363
Ctx Intensity 262.3226 +/- 90.8769
Pct Contrast 6.1188 +/- 24.0821
Cost 0.7507
RelCost 0.7183
------------------------------------
Brute force preopt -4 4 4, n = 729
0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0150 1.0150 0.0
1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0043 1.0043 0.0
2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9820 0.9820 0.0
33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9368 0.9368 0.0
138 -4.0000 0.0000 4.0000 -4.0000 0.0000 -4.0000 0.9180 0.9180 0.0
274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9110 0.9110 0.0
302 0.0000 -4.0000 4.0000 -4.0000 0.0000 4.0000 0.9033 0.9033 0.0
354 0.0000 0.0000 0.0000 -4.0000 0.0000 -4.0000 0.8991 0.8991 0.0
355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.8229 0.8229 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7507 0.7507 0.0
382 0.0000 0.0000 4.0000 -4.0000 0.0000 0.0000 0.7081 0.7081 0.0
391 0.0000 0.0000 4.0000 0.0000 0.0000 0.0000 0.7052 0.7052 0.0
Brute Force --------------------------
Min cost was 0.705212
Number of iterations 729
Search time 1.078000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 4.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 4
3 0
4 0
5 0
11 0.023 0.000 4.000 0.000 0.000 0.000 0.7051795184
13 0.015 0.000 4.000 0.000 0.000 0.000 0.7051513468
14 0.013 0.000 4.000 0.000 0.000 0.000 0.7051504575
17 0.013 1.000 4.000 0.000 0.000 0.000 0.6924597446
20 0.013 1.618 4.000 0.000 0.000 0.000 0.6914718521
22 0.013 1.385 4.000 0.000 0.000 0.000 0.6890080211
25 0.013 1.379 4.000 0.000 0.000 0.000 0.6890017834
30 0.013 1.378 4.000 0.000 0.000 0.000 0.6890010633
33 0.013 1.378 2.382 0.000 0.000 0.000 0.6035017800
39 0.013 1.378 2.253 0.000 0.000 0.000 0.6013433601
41 0.013 1.378 2.274 0.000 0.000 0.000 0.6012266425
42 0.013 1.378 2.277 0.000 0.000 0.000 0.6012238502
51 0.013 1.378 2.277 -0.087 0.000 0.000 0.6011576931
52 0.013 1.378 2.277 -0.055 0.000 0.000 0.6010799595
53 0.013 1.378 2.277 -0.050 0.000 0.000 0.6010785855
54 0.013 1.378 2.277 -0.051 0.000 0.000 0.6010782464
62 0.013 1.378 2.277 -0.051 -0.067 0.000 0.6007712362
63 0.013 1.378 2.277 -0.051 -0.066 0.000 0.6007482801
64 0.013 1.378 2.277 -0.051 -0.039 0.000 0.6005585385
66 0.013 1.378 2.277 -0.051 -0.044 0.000 0.6005396295
68 0.013 1.378 2.277 -0.051 -0.046 0.000 0.6005380611
78 0.013 1.378 2.277 -0.051 -0.046 -0.052 0.6004069124
79 0.013 1.378 2.277 -0.051 -0.046 -0.041 0.6003754225
81 0.013 1.378 2.277 -0.051 -0.046 -0.040 0.6003726800
92 -0.049 1.378 2.277 -0.051 -0.046 -0.040 0.5998837363
95 -0.053 1.378 2.277 -0.051 -0.046 -0.040 0.5998719386
96 -0.056 1.378 2.277 -0.051 -0.046 -0.040 0.5998701284
107 -0.057 1.150 2.277 -0.051 -0.046 -0.040 0.5992516852
111 -0.057 1.154 2.277 -0.051 -0.046 -0.040 0.5992505718
113 -0.057 1.153 2.277 -0.051 -0.046 -0.040 0.5992503848
114 -0.057 1.152 2.277 -0.051 -0.046 -0.040 0.5992502306
122 -0.057 1.152 2.345 -0.051 -0.046 -0.040 0.5992096489
123 -0.057 1.152 2.317 -0.051 -0.046 -0.040 0.5990236755
124 -0.057 1.152 2.313 -0.051 -0.046 -0.040 0.5990113242
126 -0.057 1.152 2.310 -0.051 -0.046 -0.040 0.5990095630
128 -0.057 1.152 2.311 -0.051 -0.046 -0.040 0.5990094638
138 -0.057 1.152 2.311 -0.044 -0.046 -0.040 0.5990043196
139 -0.057 1.152 2.311 -0.031 -0.046 -0.040 0.5989964675
141 -0.057 1.152 2.311 -0.030 -0.046 -0.040 0.5989948785
142 -0.057 1.152 2.311 -0.012 -0.046 -0.040 0.5989800368
143 -0.057 1.152 2.311 -0.011 -0.046 -0.040 0.5989797890
145 -0.057 1.152 2.311 -0.010 -0.046 -0.040 0.5989797037
155 -0.057 1.152 2.311 -0.010 -0.028 -0.040 0.5987953212
158 -0.057 1.152 2.311 -0.010 -0.029 -0.040 0.5987951987
168 -0.057 1.152 2.311 -0.010 -0.029 -0.023 0.5987117747
169 -0.057 1.152 2.311 -0.010 -0.029 -0.012 0.5987077571
170 -0.057 1.152 2.311 -0.010 -0.029 -0.016 0.5987056422
183 -0.067 1.152 2.311 -0.010 -0.029 -0.016 0.5985953749
185 -0.073 1.152 2.311 -0.010 -0.029 -0.016 0.5985776706
195 -0.073 1.203 2.311 -0.010 -0.029 -0.016 0.5984143145
196 -0.073 1.221 2.311 -0.010 -0.029 -0.016 0.5983713491
199 -0.073 1.237 2.311 -0.010 -0.029 -0.016 0.5983355187
200 -0.073 1.262 2.311 -0.010 -0.029 -0.016 0.5983127259
202 -0.073 1.254 2.311 -0.010 -0.029 -0.016 0.5983095649
204 -0.073 1.256 2.311 -0.010 -0.029 -0.016 0.5983087152
214 -0.073 1.256 2.304 -0.010 -0.029 -0.016 0.5983018492
215 -0.073 1.256 2.305 -0.010 -0.029 -0.016 0.5983017007
225 -0.073 1.256 2.305 0.010 -0.029 -0.016 0.5982206408
226 -0.073 1.256 2.305 0.027 -0.029 -0.016 0.5982097137
227 -0.073 1.256 2.305 0.021 -0.029 -0.016 0.5982062339
228 -0.073 1.256 2.305 0.020 -0.029 -0.016 0.5982059689
239 -0.073 1.256 2.305 0.020 -0.032 -0.016 0.5982048569
248 -0.073 1.256 2.305 0.020 -0.032 0.018 0.5980531274
250 -0.073 1.256 2.305 0.020 -0.032 0.028 0.5980498015
251 -0.073 1.256 2.305 0.020 -0.032 0.026 0.5980496886
252 -0.073 1.256 2.305 0.020 -0.032 0.025 0.5980496533
265 -0.064 1.256 2.305 0.020 -0.032 0.025 0.5980249701
266 -0.063 1.256 2.305 0.020 -0.032 0.025 0.5980245769
288 -0.063 1.256 2.287 0.020 -0.032 0.025 0.5980017197
290 -0.063 1.256 2.279 0.020 -0.032 0.025 0.5980013476
293 -0.063 1.256 2.276 0.020 -0.032 0.025 0.5979977186
294 -0.063 1.256 2.274 0.020 -0.032 0.025 0.5979975878
296 -0.063 1.256 2.275 0.020 -0.032 0.025 0.5979973620
305 -0.063 1.256 2.275 0.019 -0.032 0.025 0.5979956754
308 -0.063 1.256 2.275 0.015 -0.032 0.025 0.5979942349
320 -0.063 1.256 2.275 0.015 -0.041 0.025 0.5979502899
330 -0.063 1.256 2.275 0.015 -0.041 0.037 0.5978605648
332 -0.063 1.256 2.275 0.015 -0.041 0.057 0.5977882852
333 -0.063 1.256 2.275 0.015 -0.041 0.062 0.5977868339
334 -0.063 1.256 2.275 0.015 -0.041 0.061 0.5977867054
345 -0.059 1.256 2.275 0.015 -0.041 0.061 0.5977569352
346 -0.053 1.256 2.275 0.015 -0.041 0.061 0.5977442508
347 -0.054 1.256 2.275 0.015 -0.041 0.061 0.5977422235
348 -0.055 1.256 2.275 0.015 -0.041 0.061 0.5977417536
360 -0.055 1.253 2.275 0.015 -0.041 0.061 0.5977414494
362 -0.055 1.254 2.275 0.015 -0.041 0.061 0.5977412947
374 -0.055 1.254 2.270 0.015 -0.041 0.061 0.5977339584
386 -0.055 1.254 2.270 0.018 -0.041 0.061 0.5977330654
397 -0.055 1.254 2.270 0.018 -0.051 0.061 0.5977314052
398 -0.055 1.254 2.270 0.018 -0.046 0.061 0.5977246708
409 -0.055 1.254 2.270 0.018 -0.046 0.072 0.5977146423
410 -0.055 1.254 2.270 0.018 -0.046 0.069 0.5977125475
411 -0.055 1.254 2.270 0.018 -0.046 0.068 0.5977122465
438 -0.055 1.255 2.270 0.018 -0.046 0.068 0.5977119553
450 -0.055 1.255 2.272 0.018 -0.046 0.068 0.5977107105
462 -0.055 1.255 2.272 0.017 -0.046 0.068 0.5977104891
472 -0.055 1.255 2.272 0.017 -0.050 0.068 0.5977065011
484 -0.055 1.255 2.272 0.017 -0.050 0.072 0.5977044109
Powell done niters = 5
Computing relative cost
0 -25.0 -25.0 -25.0 1.028559
1 -25.0 -25.0 25.0 1.059702
2 -25.0 25.0 -25.0 1.024154
3 -25.0 25.0 25.0 1.012516
4 25.0 -25.0 -25.0 1.070341
5 25.0 -25.0 25.0 1.038172
6 25.0 25.0 -25.0 1.048788
7 25.0 25.0 25.0 1.036681
REL: 8 0.597704 8.318912 1.039864 rel = 0.574791
Number of iterations 5
Min cost was 0.597704
Number of FunctionCalls 487
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.747000 sec
Parameters at optimum (transmm) -0.05513 1.25501 2.27188
Parameters at optimum (rotdeg) 0.01705 -0.04962 0.07175
Final costs ----------------
Number of surface hits 2387
WM Intensity 240.3089 +/- 80.3061
Ctx Intensity 263.4214 +/- 91.5621
Pct Contrast 7.5264 +/- 24.8106
Cost 0.5977
RelCost 0.7183
Reg at min cost was
1.000 -0.006 -0.011 4.632;
0.011 0.025 1.000 44.476;
-0.005 -1.000 0.025 -6.486;
0.000 0.000 0.000 1.000;
Writing optimal reg to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/bbr.pass1.dat, type = 14
Original Reg
1.000 -0.006 -0.009 4.733;
0.009 0.025 1.000 43.213;
-0.006 -1.000 0.025 -8.775;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
0.000 -0.001 0.001 0.102;
-0.001 -0.000 0.000 -1.264;
-0.001 -0.000 -0.000 -2.289;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 2.561214
Computing change in rh position
Surface RMS Diff (mm) 2.599377 2.684147
mri_segreg done
mri_segreg --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --init-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/bbr.pass1.dat --out-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/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 bmdaten/Auswertung/ALS-Review/Trakula/
cd /home/bm
mri_segreg --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii --init-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/bbr.pass1.dat --out-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
sysname Linux
hostname bm-linux
machine x86_64
user bm
movvol bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/template.nii
regfile bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/tmp.bbregister.27137/bbr.pass1.dat
subject P01-a
dof 6
outregfile bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 1439983745
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 -0.006 -0.011 4.632;
0.011 0.025 1.000 44.476;
-0.005 -1.000 0.025 -6.486;
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 1.021067
1 -25.0 -25.0 25.0 1.051044
2 -25.0 25.0 -25.0 1.046868
3 -25.0 25.0 25.0 1.018075
4 25.0 -25.0 -25.0 1.049502
5 25.0 -25.0 25.0 1.053373
6 25.0 25.0 -25.0 1.040901
7 25.0 25.0 25.0 1.061767
REL: 8 0.601265 8.342595 1.042824 rel = 0.576574
Initial costs ----------------
Number of surface hits 236325
WM Intensity 239.5427 +/- 74.5815
Ctx Intensity 264.0550 +/- 91.3708
Pct Contrast 7.9048 +/- 24.5457
Cost 0.6013
RelCost 0.5766
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.6100 0.6100 0.0
3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.6078 0.6078 0.0
7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.6078 0.6078 0.0
12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.6058 0.6058 0.0
21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.6042 0.6042 0.0
30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.6024 0.6024 0.0
31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.6020 0.6020 0.0
39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.6014 0.6014 0.0
57 -0.1000 -0.1000 0.1000 -0.1000 0.0000 -0.1000 0.6012 0.6012 0.0
58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.6008 0.6008 0.0
120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.6005 0.6005 0.0
265 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.6002 0.6002 0.0
272 0.0000 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.6001 0.6001 0.0
273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.5996 0.5996 0.0
274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.5990 0.5990 0.0
283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5986 0.5986 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5977 0.5977 0.0
Brute Force --------------------------
Min cost was 0.597704
Number of iterations 729
Search time 1.089000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 0.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
7 0.146 0.000 0.000 0.000 0.000 0.000 0.6000959355
8 0.150 0.000 0.000 0.000 0.000 0.000 0.6000935778
9 0.154 0.000 0.000 0.000 0.000 0.000 0.6000922393
10 0.156 0.000 0.000 0.000 0.000 0.000 0.6000918476
12 0.163 0.000 0.000 0.000 0.000 0.000 0.6000917063
13 0.160 0.000 0.000 0.000 0.000 0.000 0.6000914838
20 0.160 -0.618 0.000 0.000 0.000 0.000 0.5940994249
22 0.160 -0.568 0.000 0.000 0.000 0.000 0.5939696124
23 0.160 -0.506 0.000 0.000 0.000 0.000 0.5939653866
25 0.160 -0.535 0.000 0.000 0.000 0.000 0.5939451906
27 0.160 -0.534 0.000 0.000 0.000 0.000 0.5939450455
38 0.160 -0.534 0.104 0.000 0.000 0.000 0.5936399919
40 0.160 -0.534 0.106 0.000 0.000 0.000 0.5936397014
42 0.160 -0.534 0.107 0.000 0.000 0.000 0.5936396472
47 0.160 -0.534 0.107 -0.618 0.000 0.000 0.5867133970
49 0.160 -0.534 0.107 -0.773 0.000 0.000 0.5864942240
50 0.160 -0.534 0.107 -0.766 0.000 0.000 0.5864927406
51 0.160 -0.534 0.107 -0.760 0.000 0.000 0.5864921625
52 0.160 -0.534 0.107 -0.758 0.000 0.000 0.5864920973
65 0.160 -0.534 0.107 -0.758 0.050 0.000 0.5863244778
66 0.160 -0.534 0.107 -0.758 0.069 0.000 0.5863086848
67 0.160 -0.534 0.107 -0.758 0.071 0.000 0.5863085000
74 0.160 -0.534 0.107 -0.758 0.071 -0.618 0.5826715059
76 0.160 -0.534 0.107 -0.758 0.071 -0.475 0.5818680860
77 0.160 -0.534 0.107 -0.758 0.071 -0.431 0.5818083912
79 0.160 -0.534 0.107 -0.758 0.071 -0.432 0.5818082110
89 0.146 -0.534 0.107 -0.758 0.071 -0.432 0.5817867259
90 0.144 -0.534 0.107 -0.758 0.071 -0.432 0.5817866455
98 0.144 -0.610 0.107 -0.758 0.071 -0.432 0.5815574157
100 0.144 -0.616 0.107 -0.758 0.071 -0.432 0.5815565846
101 0.144 -0.615 0.107 -0.758 0.071 -0.432 0.5815565527
109 0.144 -0.615 0.221 -0.758 0.071 -0.432 0.5813406995
110 0.144 -0.615 0.196 -0.758 0.071 -0.432 0.5812777011
111 0.144 -0.615 0.183 -0.758 0.071 -0.432 0.5812686731
112 0.144 -0.615 0.182 -0.758 0.071 -0.432 0.5812685829
120 0.144 -0.615 0.182 -0.807 0.071 -0.432 0.5811801680
122 0.144 -0.615 0.182 -0.821 0.071 -0.432 0.5811761978
123 0.144 -0.615 0.182 -0.820 0.071 -0.432 0.5811760951
131 0.144 -0.615 0.182 -0.820 0.109 -0.432 0.5811367442
132 0.144 -0.615 0.182 -0.820 0.104 -0.432 0.5811321037
133 0.144 -0.615 0.182 -0.820 0.099 -0.432 0.5811297042
135 0.144 -0.615 0.182 -0.820 0.098 -0.432 0.5811296706
145 0.144 -0.615 0.182 -0.820 0.098 -0.439 0.5811285776
157 0.152 -0.615 0.182 -0.820 0.098 -0.437 0.5811275397
158 0.149 -0.615 0.182 -0.820 0.098 -0.437 0.5811263578
169 0.149 -0.614 0.182 -0.820 0.098 -0.437 0.5811262880
177 0.149 -0.614 0.183 -0.820 0.098 -0.437 0.5811254234
178 0.149 -0.614 0.192 -0.820 0.098 -0.437 0.5811209341
180 0.149 -0.614 0.195 -0.820 0.098 -0.437 0.5811208127
182 0.149 -0.614 0.194 -0.820 0.098 -0.437 0.5811207896
191 0.149 -0.614 0.194 -0.824 0.098 -0.437 0.5811203183
213 0.149 -0.614 0.194 -0.823 0.098 -0.436 0.5811203010
233 0.149 -0.612 0.194 -0.823 0.098 -0.436 0.5811202544
243 0.149 -0.612 0.195 -0.823 0.098 -0.436 0.5811201839
244 0.149 -0.612 0.196 -0.823 0.098 -0.436 0.5811201722
255 0.149 -0.612 0.196 -0.827 0.098 -0.436 0.5811197728
277 0.149 -0.612 0.196 -0.827 0.098 -0.435 0.5811197583
289 0.150 -0.612 0.196 -0.827 0.098 -0.435 0.5811197281
Powell done niters = 5
Computing relative cost
0 -25.0 -25.0 -25.0 1.020635
1 -25.0 -25.0 25.0 1.053225
2 -25.0 25.0 -25.0 1.048289
3 -25.0 25.0 25.0 1.017427
4 25.0 -25.0 -25.0 1.045795
5 25.0 -25.0 25.0 1.060944
6 25.0 25.0 -25.0 1.037936
7 25.0 25.0 25.0 1.058724
REL: 8 0.581120 8.342976 1.042872 rel = 0.55723
Number of iterations 5
Min cost was 0.581120
Number of FunctionCalls 406
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 23.397000 sec
Parameters at optimum (transmm) 0.14971 -0.61227 0.19758
Parameters at optimum (rotdeg) -0.82747 0.09798 -0.43537
Final costs ----------------
Number of surface hits 236325
WM Intensity 236.5888 +/- 73.8541
Ctx Intensity 260.8884 +/- 89.8911
Pct Contrast 7.9239 +/- 24.9317
Cost 0.5811
RelCost 0.5766
Reg at min cost was
1.000 -0.007 -0.003 5.106;
0.003 0.011 1.000 43.729;
-0.007 -1.000 0.011 -6.938;
0.000 0.000 0.000 1.000;
Writing optimal reg to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat, type = 14
Original Reg
1.000 -0.006 -0.011 4.632;
0.011 0.025 1.000 44.476;
-0.005 -1.000 0.025 -6.486;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
-0.000 0.002 -0.008 -0.475;
0.008 0.014 -0.000 0.747;
0.002 0.000 0.014 0.452;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 0.725979
Computing change in rh position
Surface RMS Diff (mm) 0.840425 1.912327
mri_segreg done
tkregister2_cmdl --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz
reg file bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 -0.007 -0.003 5.106;
0.003 0.011 1.000 43.729;
-0.007 -1.000 0.011 -6.938;
0.000 0.000 0.000 1.000;
float2int = 0
---------------------------------------
INFO: loading target bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz
Tmov: --------------------
-1.797 0.000 0.000 115.000;
0.000 0.000 6.500 -61.750;
0.000 -1.797 0.000 115.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
1.000 -0.007 -0.003 5.106;
0.003 0.011 1.000 43.729;
-0.007 -1.000 0.011 -6.938;
0.000 0.000 0.000 1.000;
Determinant 1
subject = P01-a
RegMat ---------------------------
1.000 -0.007 -0.003 5.106;
0.003 0.011 1.000 43.729;
-0.007 -1.000 0.011 -6.938;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -20.9869, ref det = -1
Cleaning up
Started at Fri Aug 14 17:26:07 CEST 2015
Ended at Fri Aug 14 17:27:06 CEST 2015
BBR-Run-Time-Sec 59
bbregister Done
To check results, run:
tkregister2 --mov bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.dat --surf
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.mat -inverse bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -concat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2anatorig.mat
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/diff2anat.bbr.mat -inverse bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
terminate called after throwing an instance of 'NEWMAT::SingularException'
#-------------------------------------
#@# Inter-subject registration Fri Aug 14 17:27:06 CEST 2015
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_mni.nii.gz -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/mni2anat.mat -inverse bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat
terminate called after throwing an instance of 'NEWMAT::SingularException'
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2mni.mat -concat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2anat.mat
convert_xfm -omat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/mni2anatorig.mat -inverse bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anatorig2mni.mat
terminate called after throwing an instance of 'NEWMAT::SingularException'
#-------------------------------------
#@# Masks Fri Aug 14 17:28:45 CEST 2015
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 355000 values in range
Counting number of voxels
Found 355000 voxels in final mask
mri_binarize done
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter++.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter++.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 375068 values in range
Counting number of voxels
Found 375068 voxels in final mask
mri_binarize done
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
0 4
1 43
binval 0
binvalnot 1
Found 26664 values in range
Counting number of voxels
Found 26664 voxels in final mask
mri_binarize done
mri_aparc2aseg --s P01-a --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/
subject P01-a
outvol bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/surf/lh.white
Reading lh pial surface
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/surf/lh.pial
Loading lh annotations from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/surf/rh.white
Reading rh pial surface
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/surf/rh.pial
Loading rh annotations from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/ribbon.mgz
Loading filled from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/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 = 728369
Used brute-force search on 0 voxels
Fixing Parahip LH WM
Found 12 clusters
0 k 6.000000
1 k 449.000000
2 k 2.000000
3 k 3.000000
4 k 1.000000
5 k 2.000000
6 k 2.000000
7 k 2.000000
8 k 2.000000
9 k 1.000000
10 k 3.000000
11 k 2.000000
Fixing Parahip RH WM
Found 32 clusters
0 k 4.000000
1 k 21.000000
2 k 2.000000
3 k 265.000000
4 k 21.000000
5 k 1.000000
6 k 3.000000
7 k 6.000000
8 k 1.000000
9 k 1.000000
10 k 1.000000
11 k 1.000000
12 k 1.000000
13 k 1.000000
14 k 1.000000
15 k 1.000000
16 k 1.000000
17 k 1.000000
18 k 5.000000
19 k 3.000000
20 k 1.000000
21 k 6.000000
22 k 3.000000
23 k 7.000000
24 k 7.000000
25 k 1.000000
26 k 6.000000
27 k 5.000000
28 k 4.000000
29 k 1.000000
30 k 1.000000
31 k 1.000000
Writing output aseg to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min 1000
max 2999
binval 1
binvalnot 0
Found 399242 values in range
Counting number of voxels
Found 399242 voxels in final mask
mri_binarize done
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min 1000
max 4999
binval 1
binvalnot 0
Found 612146 values in range
Counting number of voxels
Found 612146 voxels in final mask
mri_binarize done
mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 16 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/Brain-Stem.nii.gz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/bm
cmdline mri_binarize --i bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz --match 16 --o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/Brain-Stem.nii.gz
sysname Linux
hostname bm-linux
machine x86_64
user bm
input bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
0 16
binval 1
binvalnot 0
Found 13430 values in range
Counting number of voxels
Found 13430 voxels in final mask
mri_binarize done
fslmaths bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz -add bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/Brain-Stem.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/brainmask.mgz...
crypt_gkey = *CcpE8.V7ZUkk
TR=15.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
fslmaths bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz -mul bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from bmdaten/Auswertung/ALS-Review/Trakula//P01-a/mri/aparc+aseg.mgz...
crypt_gkey = *CcpE8.V7ZUkk
TR=15.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz...
crypt_gkey = *CcpE8.V7ZUkk
fslmaths bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg_mask.nii.gz
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/White-Matter.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter++.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/White-Matter++.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter++.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter++.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter++.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/White-Matter++.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/notventricles.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/notventricles.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/notventricles.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/notventricles.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/notventricles.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/cortex.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm+bs.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm+bs.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm+bs.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm+bs.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg+2mm.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg+2mm.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg+2mm.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg_mask.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flip4fsl bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask-vent.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask-vent.nii.gz
fslorient -forceradiological bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask-vent.nii.gz
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask-vent.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat -interp nearestneighbour
terminate called after throwing an instance of 'NEWMAT::SingularException'
fslstats -t bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz -k bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}' > bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi_snr.txt
Image Exception : #22 :: ERROR: Could not open image bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/White-Matter++.flt
flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/lowb_brain_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/brain_anat_orig.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/lowb_brain_mask.nii.gz bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Fri Aug 14 17:31:28 CEST 2015
dtifit -k bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dwi.nii.gz -m bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/lowb_brain_mask.nii.gz -r bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvecs -b bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/bvals -o bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dtifit
0 128 0 128 0 19
0 slices processed
1 slices processed
2 slices processed
3 slices processed
4 slices processed
5 slices processed
6 slices processed
7 slices processed
8 slices processed
9 slices processed
10 slices processed
11 slices processed
12 slices processed
13 slices processed
14 slices processed
15 slices processed
16 slices processed
17 slices processed
18 slices processed
#-------------------------------------
#@# Priors Fri Aug 14 17:31:29 CEST 2015
/usr/local/freesurfer/bin/dmri_train --outdir bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.P01-a.25334.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dtifit_FA.nii.gz --cptdir bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
cwd /home/bm
cmdline /usr/local/freesurfer/bin/dmri_train --outdir bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.P01-a.25334.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/dtifit_FA.nii.gz --cptdir bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff --reg bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
sysname Linux
hostname bm-linux
machine x86_64
user bm
Output directory: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni
Output directory in test subject's space: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.P01-a.25334.txt
Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk
Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
FA map for output subject: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/dtifit_FA.nii.gz
Affine registration from atlas to base for output subject: /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dmri/xfms/mni2diff.bbr.mat
Number of control points for initial spline: 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5
Exclude previously chosen center streamlines: 0
Use truncated streamlines: 1
Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz
#-------------------------------------
trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015
New invocation of trac-all
Fri Aug 14 17:31:48 CEST 2015
/home/bm
/usr/local/freesurfer/bin/trac-all
-bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
Subject P01-a
SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
bm
bm-linux
Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 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 256954
maxlocks unlimited
maxsignal 256954
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 32909372 31029044 1880328 0 776996 25793220
-/+ buffers/cache: 4458828 28450544
Swap: 124999676 9000 124990676
########################################
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: 2015/08/14-15:31:48-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
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: 2015/08/14-15:31:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:31:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:31:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:31:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:31:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:31:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
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