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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.