Fri Mar 31 12:03:44 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial /usr/local/freesurfer/bin/recon-all -i /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 -T2 /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884 -s top3T_0186.fs6.3T.T2pial -all -3T -parallel -T2pial subjid top3T_0186.fs6.3T.T2pial setenv SUBJECTS_DIR /net/analyse/eirik/fs6/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux picasso 3.13.0-79-generic #123-Ubuntu SMP Fri Feb 19 14:27:58 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 514939 maxlocks unlimited maxsignal 514939 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 65933912 30415328 35518584 21076 642624 24017656 -/+ buffers/cache: 5755048 60178864 Swap: 67063804 0 67063804 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/03/31-10:03:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: top Machine: picasso Platform: Linux PlatformVersion: 3.13.0-79-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial mri_convert /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/001.mgz mri_convert.bin /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127... Starting DICOMRead2() dcmfile = /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 dcmdir = /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso Ref Series No = 3 Found 190 files, checking for dicoms Found 188 dicom files in series. First Sorting Computing Slice Direction Vs: -1 0 0 Vs: -1 0 0 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 188 ndcmfiles = 188 PE Dir = ROW (dicom read) Loading pixel data TR=8.16, TE=3.18, TI=450.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Mar 31 12:03:48 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial mri_convert --no_scale 1 /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884... Starting DICOMRead2() dcmfile = /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884 dcmdir = /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso Ref Series No = 9 Found 190 files, checking for dicoms Found 188 dicom files in series. First Sorting Computing Slice Direction Vs: -1 0 0 Vs: -1 0 0 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 188 ndcmfiles = 188 PE Dir = ROW (dicom read) Loading pixel data TR=2500.00, TE=69.15, TI=0.00, flip angle=90.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Mar 31 12:03:51 CEST 2017 Found 1 runs /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig/001.mgz /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/rawavg.mgz /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial mri_convert /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/rawavg.mgz /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig.mgz --conform mri_convert.bin /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/rawavg.mgz /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/rawavg.mgz... TR=8.16, TE=3.18, TI=450.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig.mgz... mri_add_xform_to_header -c /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/talairach.xfm /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig.mgz /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Mar 31 12:03:59 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux picasso 3.13.0-79-generic #123-Ubuntu SMP Fri Feb 19 14:27:58 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Fri Mar 31 12:03:59 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9179 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9179/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9179/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.16, TE=3.18, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9179/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Mar 31 12:04:02 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9179/nu0.mnc ./tmp.mri_nu_correct.mni.9179/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9179/0/ -iterations 1000 -distance 50 ./tmp.mri_nu_correct.mni.9179/ is a directory but not writeable [top@picasso:/net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/] [2017-03-31 12:04:03] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9179/0/ ./tmp.mri_nu_correct.mni.9179/nu0.mnc ./tmp.mri_nu_correct.mni.9179/nu1.imp 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TR=0.00, 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) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Fri Mar 31 12:06:11 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Fri Mar 31 12:06:11 CEST 2017 Ended at Fri Mar 31 12:06:51 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Mar 31 12:06:53 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6141, pval=0.2817 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/talairach_avi.log tal_QC_AZS /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/talairach_avi.log TalAviQA: 0.93438 z-score: -9 #-------------------------------------------- #@# Nu Intensity Correction Fri Mar 31 12:06:53 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux picasso 3.13.0-79-generic #123-Ubuntu SMP Fri Feb 19 14:27:58 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Fri Mar 31 12:06:53 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.14450 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14450/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.14450/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.16, TE=3.18, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.14450/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Mar 31 12:06:57 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.14450/nu0.mnc ./tmp.mri_nu_correct.mni.14450/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14450/0/ -iterations 1000 -distance 50 ./tmp.mri_nu_correct.mni.14450/ is a directory but not writeable [top@picasso:/net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/] [2017-03-31 12:06:57] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14450/0/ ./tmp.mri_nu_correct.mni.14450/nu0.mnc ./tmp.mri_nu_correct.mni.14450/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 90 CV of field change: 0.000995844 ./tmp.mri_nu_correct.mni.14450/0/ is a directory but not writeable mri_binarize --i ./tmp.mri_nu_correct.mni.14450/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14450/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.14450/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14450/ones.mgz sysname Linux hostname picasso machine x86_64 user top input ./tmp.mri_nu_correct.mni.14450/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14450/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14450/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14450/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14450/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14450/input.mean.dat sysname Linux hostname picasso machine x86_64 user top UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14450/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.14450/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14450/ones.mgz --i ./tmp.mri_nu_correct.mni.14450/nu1.mnc --sum ./tmp.mri_nu_correct.mni.14450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14450/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14450/ones.mgz --i ./tmp.mri_nu_correct.mni.14450/nu1.mnc --sum ./tmp.mri_nu_correct.mni.14450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14450/output.mean.dat sysname Linux hostname picasso machine x86_64 user top UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14450/ones.mgz Loading ./tmp.mri_nu_correct.mni.14450/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.14450/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.14450/nu1.mnc ./tmp.mri_nu_correct.mni.14450/nu1.mnc mul 1.02992112062445999639 Saving result to './tmp.mri_nu_correct.mni.14450/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.14450/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.14450/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.14450/nu1.mnc... TR=0.00, 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) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (12, 113) to ( 3, 110) Fri Mar 31 12:09:33 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Mar 31 12:09:34 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 0.97726 0.01364 0.01144 10.14998; -0.00826 0.98151 0.17126 -26.67592; -0.05127 -0.31480 0.98507 8.08731; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 105 gm peak at 64 (64), valley at 42 (42) csf peak at 10, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 63 (63), valley at 39 (39) csf peak at 10, setting threshold to 45 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 21 seconds. #-------------------------------------------- #@# Skull Stripping Fri Mar 31 12:11:55 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_em_register -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=27.1 skull bounding box = (49, 12, 17) --> (201, 246, 152) using (100, 90, 85) as brain centroid... mean wm in atlas = 108, using box (81,61,68) --> (118, 118,101) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 101 +- 7.5 after smoothing, mri peak at 101, scaling input intensities by 1.069 scaling channel 0 by 1.06931 initial log_p = -4.830 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.613442 @ (-9.091, 27.273, 9.091) max log p = -4.425973 @ (4.545, 4.545, -13.636) max log p = -4.406451 @ (6.818, 2.273, 2.273) max log p = -4.386540 @ (-1.136, -1.136, -1.136) max log p = -4.372315 @ (-0.568, -0.568, 0.568) max log p = -4.365918 @ (-2.557, 0.284, -3.125) Found translation: (-2.0, 32.7, -6.0): log p = -4.366 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.183, old_max_log_p =-4.366 (thresh=-4.4) 1.05465 0.05313 -0.12828 0.49059; 0.00000 1.14215 0.47309 -22.20735; 0.16136 -0.46905 1.13237 14.86522; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.183, old_max_log_p =-4.183 (thresh=-4.2) 1.05465 0.05313 -0.12828 0.49059; 0.00000 1.14215 0.47309 -22.20735; 0.16136 -0.46905 1.13237 14.86522; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.131, old_max_log_p =-4.183 (thresh=-4.2) 1.06399 0.05984 -0.00292 -13.01555; -0.05914 1.23613 0.33609 -11.03651; 0.05157 -0.30443 1.12452 11.22818; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.130, old_max_log_p =-4.131 (thresh=-4.1) 1.07912 0.11010 -0.03236 -16.68120; -0.09710 1.25053 0.26300 -1.59273; 0.08238 -0.22085 1.14338 -4.90685; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.117, old_max_log_p =-4.130 (thresh=-4.1) 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.117, old_max_log_p =-4.117 (thresh=-4.1) 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.117 (old=-4.830) transform before final EM align: 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000 final transform: 1.08169 0.10203 -0.04397 -14.88390; -0.08748 1.24810 0.27165 -3.51068; 0.09183 -0.22965 1.13821 -4.61232; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1368.328238 mri_em_register stimesec 1.982424 mri_em_register ru_maxrss 609532 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 786729 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 161 mri_em_register ru_nivcsw 116524 registration took 6 minutes and 30 seconds. mri_watershed -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=76 z=104 r=83 first estimation of the main basin volume: 2437571 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=148, y=74, z=74, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=7416854986 voxels, voxel volume =1.000 = 7416854986 mmm3 = 7416855.040 cm3 done. PostAnalyze...Basin Prior 197 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=87, z=100, r=9868 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=55 , nb = 44165 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1030282215 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 1078605584 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=74 , nb = -1056044059 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=52 , nb = 1083000172 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 1065905328 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 55, 39, 32, 59 after analyzing : 29, 39, 39, 44 RIGHT_CER before analyzing : 20, 68, 85, 91 after analyzing : 20, 79, 85, 82 LEFT_CER before analyzing : 19, 60, 83, 92 after analyzing : 19, 75, 83, 79 RIGHT_BRAIN before analyzing : 74, 41, 30, 56 after analyzing : 31, 41, 41, 44 LEFT_BRAIN before analyzing : 52, 42, 38, 59 after analyzing : 31, 42, 42, 46 OTHER before analyzing : 28, 41, 47, 54 after analyzing : 28, 45, 47, 47 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 70.545, std = 8.440 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 6.37, sigma = 11.04 after rotation: sse = 6.37, sigma = 11.04 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.12, its var is 18.40 before Erosion-Dilatation 4.29% of inacurate vertices after Erosion-Dilatation 3.46% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...52 iterations mri_strip_skull: done peeling brain Brain Size = 1719713 voxels, voxel volume = 1.000 mm3 = 1719713 mmm3 = 1719.713 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 28.555384 mri_watershed stimesec 0.475523 mri_watershed ru_maxrss 825348 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 390625 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2888 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 8357 mri_watershed ru_nivcsw 3081 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Mar 31 12:18:51 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_em_register -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (55, 19, 29) --> (194, 170, 175) using (101, 69, 102) as brain centroid... mean wm in atlas = 107, using box (84,50,84) --> (118, 87,119) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 102 +- 6.8 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -4.733 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.338879 @ (-9.091, 27.273, -9.091) max log p = -4.020159 @ (4.545, 4.545, 4.545) max log p = -3.973423 @ (2.273, 2.273, 2.273) max log p = -3.949360 @ (1.136, -3.409, -1.136) max log p = -3.927507 @ (0.568, 0.568, -0.568) max log p = -3.927507 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 31.2, -4.0): log p = -3.928 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.872, old_max_log_p =-3.928 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.03837 0.27823 4.92745; 0.00000 -0.25882 0.96593 30.03761; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.872, old_max_log_p =-3.872 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.03837 0.27823 4.92745; 0.00000 -0.25882 0.96593 30.03761; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.762, old_max_log_p =-3.872 (thresh=-3.9) 1.01275 -0.00789 -0.10302 8.93015; 0.03105 0.98873 0.22844 6.42820; 0.09921 -0.22473 0.96944 14.09530; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.760, old_max_log_p =-3.762 (thresh=-3.8) 0.99423 0.02400 -0.09370 5.70243; -0.00214 1.00699 0.23603 8.30043; 0.09735 -0.22052 0.95126 15.80810; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.733, old_max_log_p =-3.760 (thresh=-3.8) 0.99539 0.02403 -0.09381 5.56092; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.731, old_max_log_p =-3.733 (thresh=-3.7) 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.731 (old=-4.733) transform before final EM align: 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1099.271216 mri_em_register stimesec 1.986300 mri_em_register ru_maxrss 600368 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 848764 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 2888 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 204 mri_em_register ru_nivcsw 97174 registration took 5 minutes and 4 seconds. #-------------------------------------- #@# CA Normalize Fri Mar 31 12:23:55 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (55, 19, 29) --> (194, 170, 175) using (101, 69, 102) as brain centroid... mean wm in atlas = 107, using box (84,50,84) --> (118, 87,119) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 102 +- 6.8 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 246344 sample points... INFO: compute sample coordinates transform 0.99422 0.02400 -0.09370 5.70292; -0.00135 1.00751 0.24436 7.31069; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (121, 22, 24) --> (195, 136, 190) Left_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 4 of 52 (7.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 22, 25) --> (134, 131, 193) Right_Cerebral_White_Matter: limiting intensities to 105.0 --> 132.0 4 of 9 (44.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 112, 52) --> (175, 154, 107) Left_Cerebellum_White_Matter: limiting intensities to 124.0 --> 132.0 14 of 16 (87.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 112, 53) --> (126, 151, 111) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 3 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 97, 90) --> (146, 166, 121) Brain_Stem: limiting intensities to 136.0 --> 132.0 5 of 5 (100.0%) samples deleted using 85 total control points for intensity normalization... bias field = 0.943 +- 0.075 0 of 58 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (121, 22, 24) --> (195, 136, 190) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 29 of 99 (29.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 22, 25) --> (134, 131, 193) Right_Cerebral_White_Matter: limiting intensities to 122.0 --> 132.0 80 of 85 (94.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 112, 52) --> (175, 154, 107) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 16 of 52 (30.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 112, 53) --> (126, 151, 111) Right_Cerebellum_White_Matter: limiting intensities to 120.0 --> 132.0 54 of 69 (78.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 97, 90) --> (146, 166, 121) Brain_Stem: limiting intensities to 118.0 --> 132.0 41 of 57 (71.9%) samples deleted using 362 total control points for intensity normalization... bias field = 0.862 +- 0.150 0 of 141 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (121, 22, 24) --> (195, 136, 190) Left_Cerebral_White_Matter: limiting intensities to 110.0 --> 132.0 221 of 242 (91.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 22, 25) --> (134, 131, 193) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 100 of 223 (44.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 112, 52) --> (175, 154, 107) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 97 (48.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 112, 53) --> (126, 151, 111) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 43 of 58 (74.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 97, 90) --> (146, 166, 121) Brain_Stem: limiting intensities to 88.0 --> 132.0 30 of 68 (44.1%) samples deleted using 688 total control points for intensity normalization... bias field = 0.974 +- 0.121 0 of 244 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 2 seconds. #-------------------------------------- #@# CA Reg Fri Mar 31 12:25:57 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_ca_register -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.02 (predicted orig area = 7.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.034, neg=0, invalid=762 0001: dt=295.936000, rms=0.910 (11.987%), neg=0, invalid=762 0002: dt=221.952000, rms=0.878 (3.528%), neg=0, invalid=762 0003: dt=295.936000, rms=0.861 (1.942%), neg=0, invalid=762 0004: dt=167.602210, rms=0.850 (1.226%), neg=0, invalid=762 0005: dt=369.920000, rms=0.842 (1.003%), neg=0, invalid=762 0006: dt=139.967480, rms=0.837 (0.622%), neg=0, invalid=762 0007: dt=517.888000, rms=0.829 (0.889%), neg=0, invalid=762 0008: dt=129.472000, rms=0.826 (0.358%), neg=0, invalid=762 0009: dt=1479.680000, rms=0.817 (1.161%), neg=0, invalid=762 0010: dt=110.976000, rms=0.810 (0.774%), neg=0, invalid=762 0011: dt=2071.552000, rms=0.798 (1.520%), neg=0, invalid=762 0012: dt=141.948718, rms=0.795 (0.425%), neg=0, invalid=762 0013: dt=369.920000, rms=0.793 (0.178%), neg=0, invalid=762 0014: dt=369.920000, rms=0.793 (0.035%), neg=0, invalid=762 0015: dt=369.920000, rms=0.792 (0.129%), neg=0, invalid=762 0016: dt=369.920000, rms=0.786 (0.734%), neg=0, invalid=762 0017: dt=369.920000, rms=0.782 (0.554%), neg=0, invalid=762 0018: dt=369.920000, rms=0.779 (0.386%), neg=0, invalid=762 0019: dt=369.920000, rms=0.776 (0.347%), neg=0, invalid=762 0020: dt=369.920000, rms=0.774 (0.322%), neg=0, invalid=762 0021: dt=369.920000, rms=0.770 (0.500%), neg=0, invalid=762 0022: dt=369.920000, rms=0.767 (0.358%), neg=0, invalid=762 0023: dt=369.920000, rms=0.765 (0.203%), neg=0, invalid=762 0024: dt=369.920000, rms=0.764 (0.181%), neg=0, invalid=762 0025: dt=369.920000, rms=0.763 (0.150%), neg=0, invalid=762 0026: dt=369.920000, rms=0.762 (0.149%), neg=0, invalid=762 0027: dt=369.920000, rms=0.760 (0.170%), neg=0, invalid=762 0028: dt=369.920000, rms=0.760 (0.083%), neg=0, invalid=762 0029: dt=369.920000, rms=0.759 (0.045%), neg=0, invalid=762 0030: dt=129.472000, rms=0.759 (0.112%), neg=0, invalid=762 0031: dt=517.888000, rms=0.758 (0.095%), neg=0, invalid=762 0032: dt=517.888000, rms=0.758 (-0.529%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.759, neg=0, invalid=762 0033: dt=129.472000, rms=0.757 (0.273%), neg=0, invalid=762 0034: dt=129.472000, rms=0.756 (0.039%), neg=0, invalid=762 0035: dt=129.472000, rms=0.756 (0.010%), neg=0, invalid=762 0036: dt=129.472000, rms=0.756 (0.002%), neg=0, invalid=762 0037: dt=129.472000, rms=0.756 (0.003%), neg=0, invalid=762 0038: dt=129.472000, rms=0.756 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.773, neg=0, invalid=762 0039: dt=124.416000, rms=0.766 (0.893%), neg=0, invalid=762 0040: dt=234.396624, rms=0.755 (1.478%), neg=0, invalid=762 0041: dt=66.478649, rms=0.750 (0.638%), neg=0, invalid=762 0042: dt=145.152000, rms=0.745 (0.706%), neg=0, invalid=762 0043: dt=414.720000, rms=0.739 (0.795%), neg=0, invalid=762 0044: dt=62.208000, rms=0.733 (0.750%), neg=0, invalid=762 0045: dt=145.152000, rms=0.731 (0.283%), neg=0, invalid=762 0046: dt=145.152000, rms=0.729 (0.306%), neg=0, invalid=762 0047: dt=82.944000, rms=0.728 (0.142%), neg=0, invalid=762 0048: dt=82.944000, rms=0.727 (0.171%), neg=0, invalid=762 0049: dt=82.944000, rms=0.725 (0.256%), neg=0, invalid=762 0050: dt=82.944000, rms=0.722 (0.331%), neg=0, invalid=762 0051: dt=82.944000, rms=0.720 (0.350%), neg=0, invalid=762 0052: dt=82.944000, rms=0.717 (0.414%), neg=0, invalid=762 0053: dt=82.944000, rms=0.714 (0.402%), neg=0, invalid=762 0054: dt=82.944000, rms=0.711 (0.396%), neg=0, invalid=762 0055: dt=82.944000, rms=0.709 (0.300%), neg=0, invalid=762 0056: dt=82.944000, rms=0.707 (0.304%), neg=0, invalid=762 0057: dt=82.944000, rms=0.705 (0.256%), neg=0, invalid=762 0058: dt=82.944000, rms=0.703 (0.210%), neg=0, invalid=762 0059: dt=82.944000, rms=0.702 (0.143%), neg=0, invalid=762 0060: dt=41.472000, rms=0.702 (0.031%), neg=0, invalid=762 0061: dt=41.472000, rms=0.702 (0.009%), neg=0, invalid=762 0062: dt=36.288000, rms=0.702 (0.004%), neg=0, invalid=762 0063: dt=36.288000, rms=0.702 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0064: dt=31.104000, rms=0.702 (0.189%), neg=0, invalid=762 0065: dt=0.001582, rms=0.702 (0.002%), neg=0, invalid=762 0066: dt=0.001582, rms=0.702 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.751, neg=0, invalid=762 0067: dt=9.600000, rms=0.748 (0.323%), neg=0, invalid=762 0068: dt=6.400000, rms=0.748 (0.036%), neg=0, invalid=762 0069: dt=6.400000, rms=0.748 (0.006%), neg=0, invalid=762 0070: dt=6.400000, rms=0.748 (-0.094%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.749, neg=0, invalid=762 0071: dt=0.000000, rms=0.748 (0.146%), neg=0, invalid=762 0072: dt=0.000000, rms=0.748 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.859, neg=0, invalid=762 0073: dt=6.580882, rms=0.835 (2.778%), neg=0, invalid=762 0074: dt=7.351682, rms=0.830 (0.606%), neg=0, invalid=762 0075: dt=11.520000, rms=0.828 (0.274%), neg=0, invalid=762 0076: dt=16.128000, rms=0.826 (0.239%), neg=0, invalid=762 0077: dt=16.128000, rms=0.826 (-0.139%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.827, neg=0, invalid=762 0078: dt=0.000000, rms=0.826 (0.103%), neg=0, invalid=762 0079: dt=0.000000, rms=0.826 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.898, neg=0, invalid=762 0080: dt=0.000000, rms=0.897 (0.087%), neg=0, invalid=762 0081: dt=0.000000, rms=0.897 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.898, neg=0, invalid=762 0082: dt=0.000000, rms=0.897 (0.087%), neg=0, invalid=762 0083: dt=0.000000, rms=0.897 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.776, neg=0, invalid=762 0084: dt=0.880829, rms=0.755 (2.683%), neg=0, invalid=762 0085: dt=0.096000, rms=0.754 (0.141%), neg=0, invalid=762 0086: dt=0.096000, rms=0.754 (-0.098%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.755, neg=0, invalid=762 0087: dt=0.048000, rms=0.754 (0.151%), neg=0, invalid=762 0088: dt=0.006000, rms=0.754 (0.003%), neg=0, invalid=762 0089: dt=0.006000, rms=0.754 (0.001%), neg=0, invalid=762 0090: dt=0.006000, rms=0.754 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.08033 (27) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1563 voxels, overlap=0.614) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1563 voxels, peak = 26), gca=26.1 gca peak = 0.15565 (16) mri peak = 0.06623 (16) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (530 voxels, overlap=0.807) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (530 voxels, peak = 18), gca=17.5 gca peak = 0.26829 (96) mri peak = 0.15164 (75) Right_Pallidum (52): linear fit = 0.79 x + 0.0 (240 voxels, overlap=0.015) Right_Pallidum (52): linear fit = 0.79 x + 0.0 (240 voxels, peak = 75), gca=75.4 gca peak = 0.20183 (93) mri peak = 0.07692 (76) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (97 voxels, overlap=0.449) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (97 voxels, peak = 82), gca=82.3 gca peak = 0.21683 (55) mri peak = 0.06311 (86) Right_Hippocampus (53): linear fit = 1.49 x + 0.0 (392 voxels, overlap=0.016) Right_Hippocampus (53): linear fit = 1.49 x + 0.0 (392 voxels, peak = 82), gca=81.7 gca peak = 0.30730 (58) mri peak = 0.04982 (72) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (376 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (376 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.06038 (96) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (60073 voxels, overlap=0.977) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (60073 voxels, peak = 102), gca=101.5 gca peak = 0.12076 (102) mri peak = 0.06094 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (59789 voxels, overlap=0.943) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (59789 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.03270 (65) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (18526 voxels, overlap=0.905) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (18526 voxels, peak = 65), gca=64.6 gca peak = 0.15082 (58) mri peak = 0.03552 (56) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21045 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21045 voxels, peak = 59), gca=59.4 gca peak = 0.14161 (67) mri peak = 0.07898 (73) Right_Caudate (50): linear fit = 1.05 x + 0.0 (389 voxels, overlap=0.688) Right_Caudate (50): linear fit = 1.05 x + 0.0 (389 voxels, peak = 71), gca=70.7 gca peak = 0.15243 (71) mri peak = 0.06822 (94) Left_Caudate (11): linear fit = 1.25 x + 0.0 (894 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.25 x + 0.0 (894 voxels, peak = 89), gca=89.1 gca peak = 0.13336 (57) mri peak = 0.02610 (64) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (35094 voxels, overlap=0.004) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (35094 voxels, peak = 66), gca=66.4 gca peak = 0.13252 (56) mri peak = 0.02200 (38) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (34911 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (34911 voxels, peak = 66), gca=66.4 gca peak = 0.18181 (84) mri peak = 0.04046 (78) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (12138 voxels, overlap=0.974) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (12138 voxels, peak = 81), gca=81.1 gca peak = 0.20573 (83) mri peak = 0.03081 (50) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (9143 voxels, overlap=0.059) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (9143 voxels, peak = 80), gca=80.1 gca peak = 0.21969 (57) mri peak = 0.05000 (55) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (150 voxels, overlap=0.523) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (150 voxels, peak = 72), gca=72.1 gca peak = 0.39313 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14181 (85) mri peak = 0.06268 (79) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3068 voxels, overlap=0.969) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3068 voxels, peak = 82), gca=82.0 gca peak = 0.11978 (83) mri peak = 0.09968 (75) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2055 voxels, overlap=0.848) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2055 voxels, peak = 79), gca=79.3 gca peak = 0.13399 (79) mri peak = 0.04960 (72) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1370 voxels, overlap=0.901) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1370 voxels, peak = 74), gca=73.9 gca peak = 0.14159 (79) mri peak = 0.05464 (78) Right_Putamen (51): linear fit = 1.04 x + 0.0 (604 voxels, overlap=0.900) Right_Putamen (51): linear fit = 1.04 x + 0.0 (604 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.09833 (81) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9442 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9442 voxels, peak = 85), gca=85.2 gca peak = 0.13281 (86) mri peak = 0.08238 (89) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (690 voxels, overlap=0.726) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (690 voxels, peak = 88), gca=88.2 gca peak = 0.12801 (89) mri peak = 0.06516 (90) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (716 voxels, overlap=0.752) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (716 voxels, peak = 90), gca=90.3 gca peak = 0.20494 (23) mri peak = 0.09103 (45) gca peak = 0.15061 (21) mri peak = 0.08276 (16) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (458 voxels, overlap=0.378) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (458 voxels, peak = 14), gca=14.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Amygdala = 0.39313 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Amygdala based on Left_Amygdala = 1.26 x + 0: 72 estimating mean gm scale to be 1.23 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.754, neg=0, invalid=762 0091: dt=129.472000, rms=0.746 (1.100%), neg=0, invalid=762 0092: dt=295.936000, rms=0.742 (0.509%), neg=0, invalid=762 0093: dt=129.472000, rms=0.740 (0.258%), neg=0, invalid=762 0094: dt=369.920000, rms=0.738 (0.275%), neg=0, invalid=762 0095: dt=129.472000, rms=0.736 (0.217%), neg=0, invalid=762 0096: dt=129.472000, rms=0.736 (0.068%), neg=0, invalid=762 0097: dt=443.904000, rms=0.734 (0.198%), neg=0, invalid=762 0098: dt=92.480000, rms=0.734 (0.103%), neg=0, invalid=762 0099: dt=517.888000, rms=0.732 (0.253%), neg=0, invalid=762 0100: dt=92.480000, rms=0.731 (0.039%), neg=0, invalid=762 0101: dt=2.890000, rms=0.731 (0.002%), neg=0, invalid=762 0102: dt=1.445000, rms=0.731 (0.001%), neg=0, invalid=762 0103: dt=0.722500, rms=0.731 (0.000%), neg=0, invalid=762 0104: dt=0.505750, rms=0.731 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0105: dt=0.126438, rms=0.731 (0.161%), neg=0, invalid=762 0106: dt=0.031609, rms=0.731 (0.000%), neg=0, invalid=762 0107: dt=0.015805, rms=0.731 (0.000%), neg=0, invalid=762 0108: dt=0.001976, rms=0.731 (0.000%), neg=0, invalid=762 0109: dt=0.000247, rms=0.731 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0110: dt=0.000000, rms=0.732 (0.161%), neg=0, invalid=762 0111: dt=0.000000, rms=0.732 (0.000%), neg=0, invalid=762 0112: dt=0.000014, rms=0.732 (0.000%), neg=0, invalid=762 0113: dt=0.000007, rms=0.732 (0.000%), neg=0, invalid=762 0114: dt=0.000003, rms=0.732 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0115: dt=0.000000, rms=0.732 (0.161%), neg=0, invalid=762 0116: dt=0.000000, rms=0.732 (0.000%), neg=0, invalid=762 0117: dt=0.000003, rms=0.732 (0.000%), neg=0, invalid=762 0118: dt=0.000001, rms=0.732 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0119: dt=2.800000, rms=0.728 (0.747%), neg=0, invalid=762 0120: dt=0.010937, rms=0.728 (0.006%), neg=0, invalid=762 0121: dt=0.010937, rms=0.728 (0.002%), neg=0, invalid=762 0122: dt=0.000342, rms=0.728 (0.001%), neg=0, invalid=762 0123: dt=0.000085, rms=0.728 (0.000%), neg=0, invalid=762 0124: dt=0.000000, rms=0.728 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0125: dt=0.000000, rms=0.728 (0.165%), neg=0, invalid=762 0126: dt=0.000000, rms=0.728 (0.000%), neg=0, invalid=762 0127: dt=0.000244, rms=0.728 (0.000%), neg=0, invalid=762 0128: dt=0.000122, rms=0.728 (0.000%), neg=0, invalid=762 0129: dt=0.000061, rms=0.728 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=762 0130: dt=1.008000, rms=0.724 (0.978%), neg=0, invalid=762 0131: dt=1.008000, rms=0.718 (0.779%), neg=0, invalid=762 0132: dt=1.008000, rms=0.713 (0.738%), neg=0, invalid=762 0133: dt=0.003375, rms=0.713 (0.003%), neg=0, invalid=762 0134: dt=0.000003, rms=0.713 (0.000%), neg=0, invalid=762 0135: dt=0.000002, rms=0.713 (0.000%), neg=0, invalid=762 0136: dt=0.000001, rms=0.713 (0.000%), neg=0, invalid=762 0137: dt=0.000000, rms=0.713 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 0138: dt=0.000000, rms=0.713 (0.165%), neg=0, invalid=762 0139: dt=0.000000, rms=0.713 (0.000%), neg=0, invalid=762 0140: dt=0.000009, rms=0.713 (0.000%), neg=0, invalid=762 0141: dt=0.000001, rms=0.713 (0.000%), neg=0, invalid=762 0142: dt=0.000000, rms=0.713 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0143: dt=1.792000, rms=0.700 (2.592%), neg=0, invalid=762 0144: dt=1.792000, rms=0.690 (1.480%), neg=0, invalid=762 0145: dt=1.792000, rms=0.683 (0.907%), neg=0, invalid=762 0146: dt=1.536000, rms=0.680 (0.505%), neg=0, invalid=762 0147: dt=0.448000, rms=0.679 (0.111%), neg=0, invalid=762 0148: dt=0.028000, rms=0.679 (0.007%), neg=0, invalid=762 0149: dt=0.028000, rms=0.679 (0.006%), neg=0, invalid=762 0150: dt=0.001750, rms=0.679 (0.000%), neg=0, invalid=762 0151: dt=0.000109, rms=0.679 (0.000%), neg=0, invalid=762 0152: dt=0.000000, rms=0.679 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0153: dt=1.792000, rms=0.675 (0.821%), neg=0, invalid=762 0154: dt=1.792000, rms=0.672 (0.456%), neg=0, invalid=762 0155: dt=1.792000, rms=0.669 (0.336%), neg=0, invalid=762 0156: dt=1.792000, rms=0.668 (0.263%), neg=0, invalid=762 0157: dt=1.792000, rms=0.666 (0.218%), neg=0, invalid=762 0158: dt=1.792000, rms=0.665 (0.181%), neg=0, invalid=762 0159: dt=2.250000, rms=0.664 (0.195%), neg=0, invalid=762 0160: dt=1.792000, rms=0.663 (0.132%), neg=0, invalid=762 0161: dt=1.792000, rms=0.662 (0.106%), neg=0, invalid=762 0162: dt=1.792000, rms=0.661 (0.105%), neg=0, invalid=762 0163: dt=1.792000, rms=0.661 (0.087%), neg=0, invalid=762 0164: dt=1.792000, rms=0.660 (0.081%), neg=0, invalid=762 0165: dt=1.792000, rms=0.660 (0.074%), neg=0, invalid=762 0166: dt=1.792000, rms=0.659 (0.068%), neg=0, invalid=762 0167: dt=1.792000, rms=0.659 (0.061%), neg=0, invalid=762 0168: dt=1.792000, rms=0.658 (0.054%), neg=0, invalid=762 0169: dt=1.792000, rms=0.658 (0.052%), neg=0, invalid=762 0170: dt=1.792000, rms=0.658 (0.048%), neg=0, invalid=762 0171: dt=1.792000, rms=0.658 (0.045%), neg=0, invalid=762 0172: dt=1.792000, rms=0.657 (0.078%), neg=0, invalid=762 0173: dt=1.792000, rms=0.656 (0.107%), neg=0, invalid=762 0174: dt=1.792000, rms=0.656 (0.127%), neg=0, invalid=762 0175: dt=1.792000, rms=0.655 (0.132%), neg=0, invalid=762 0176: dt=1.792000, rms=0.654 (0.124%), neg=0, invalid=762 0177: dt=1.792000, rms=0.653 (0.104%), neg=0, invalid=762 0178: dt=1.792000, rms=0.653 (-0.004%), neg=0, invalid=762 0179: dt=0.000000, rms=0.653 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0180: dt=0.448000, rms=0.624 (3.021%), neg=0, invalid=762 0181: dt=0.285714, rms=0.621 (0.578%), neg=0, invalid=762 0182: dt=0.320000, rms=0.618 (0.512%), neg=0, invalid=762 0183: dt=0.112000, rms=0.617 (0.116%), neg=0, invalid=762 0184: dt=0.112000, rms=0.616 (0.113%), neg=0, invalid=762 0185: dt=0.320000, rms=0.614 (0.292%), neg=0, invalid=762 0186: dt=0.112000, rms=0.614 (0.074%), neg=0, invalid=762 0187: dt=0.320000, rms=0.613 (0.193%), neg=0, invalid=762 0188: dt=0.320000, rms=0.612 (0.147%), neg=0, invalid=762 0189: dt=0.320000, rms=0.611 (0.125%), neg=0, invalid=762 0190: dt=0.320000, rms=0.610 (0.100%), neg=0, invalid=762 0191: dt=0.112000, rms=0.610 (0.033%), neg=0, invalid=762 0192: dt=0.112000, rms=0.610 (0.041%), neg=0, invalid=762 0193: dt=0.112000, rms=0.610 (0.063%), neg=0, invalid=762 0194: dt=0.112000, rms=0.609 (0.075%), neg=0, invalid=762 0195: dt=0.112000, rms=0.609 (0.088%), neg=0, invalid=762 0196: dt=0.112000, rms=0.608 (0.090%), neg=0, invalid=762 0197: dt=0.112000, rms=0.607 (0.087%), neg=0, invalid=762 0198: dt=0.112000, rms=0.607 (0.088%), neg=0, invalid=762 0199: dt=0.112000, rms=0.606 (0.083%), neg=0, invalid=762 0200: dt=0.112000, rms=0.606 (0.076%), neg=0, invalid=762 0201: dt=0.112000, rms=0.606 (0.060%), neg=0, invalid=762 0202: dt=0.112000, rms=0.605 (0.046%), neg=0, invalid=762 0203: dt=0.112000, rms=0.605 (0.036%), neg=0, invalid=762 0204: dt=0.112000, rms=0.605 (0.028%), neg=0, invalid=762 0205: dt=0.112000, rms=0.605 (0.012%), neg=0, invalid=762 0206: dt=0.112000, rms=0.605 (0.009%), neg=0, invalid=762 0207: dt=0.000000, rms=0.605 (0.002%), neg=0, invalid=762 0208: dt=0.050000, rms=0.605 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0209: dt=0.112000, rms=0.602 (0.577%), neg=0, invalid=762 0210: dt=0.112000, rms=0.601 (0.307%), neg=0, invalid=762 0211: dt=0.112000, rms=0.599 (0.248%), neg=0, invalid=762 0212: dt=0.203125, rms=0.597 (0.346%), neg=0, invalid=762 0213: dt=0.112000, rms=0.596 (0.120%), neg=0, invalid=762 0214: dt=0.112000, rms=0.596 (0.098%), neg=0, invalid=762 0215: dt=0.112000, rms=0.595 (0.072%), neg=0, invalid=762 0216: dt=0.112000, rms=0.595 (0.061%), neg=0, invalid=762 0217: dt=0.112000, rms=0.595 (0.043%), neg=0, invalid=762 0218: dt=0.112000, rms=0.595 (0.037%), neg=0, invalid=762 0219: dt=0.112000, rms=0.594 (0.055%), neg=0, invalid=762 0220: dt=0.112000, rms=0.594 (0.055%), neg=0, invalid=762 0221: dt=0.112000, rms=0.594 (0.039%), neg=0, invalid=762 0222: dt=0.112000, rms=0.594 (0.000%), neg=0, invalid=762 0223: dt=0.112000, rms=0.594 (-0.037%), neg=0, invalid=762 0224: dt=0.000000, rms=0.594 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0225: dt=0.000000, rms=0.590 (0.207%), neg=0, invalid=762 0226: dt=0.000000, rms=0.590 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0227: dt=0.000000, rms=0.590 (0.207%), neg=0, invalid=762 0228: dt=0.000000, rms=0.590 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0229: dt=16.657534, rms=0.589 (0.280%), neg=0, invalid=762 0230: dt=7.776000, rms=0.589 (0.005%), neg=0, invalid=762 0231: dt=7.776000, rms=0.589 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 0232: dt=36.288000, rms=0.588 (0.342%), neg=0, invalid=762 0233: dt=62.208000, rms=0.588 (0.149%), neg=0, invalid=762 0234: dt=62.208000, rms=0.588 (-0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.589, neg=0, invalid=762 iter 0, gcam->neg = 17 after 5 iterations, nbhd size=0, neg = 0 0235: dt=19.200000, rms=0.584 (0.874%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 5 iterations, nbhd size=0, neg = 0 0236: dt=11.200000, rms=0.583 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 16 iterations, nbhd size=1, neg = 0 0237: dt=11.200000, rms=0.583 (-0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=1, neg = 0 0238: dt=30.237454, rms=0.578 (1.136%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0239: dt=32.000000, rms=0.574 (0.602%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0240: dt=11.200000, rms=0.573 (0.263%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 13 iterations, nbhd size=1, neg = 0 0241: dt=84.528302, rms=0.571 (0.377%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=0, neg = 0 0242: dt=26.476190, rms=0.569 (0.366%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0243: dt=11.200000, rms=0.568 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0244: dt=11.200000, rms=0.567 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0245: dt=11.200000, rms=0.567 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 5 iterations, nbhd size=0, neg = 0 0246: dt=11.200000, rms=0.566 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0247: dt=11.200000, rms=0.565 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 16 iterations, nbhd size=1, neg = 0 0248: dt=11.200000, rms=0.564 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0249: dt=11.200000, rms=0.564 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 18 iterations, nbhd size=1, neg = 0 0250: dt=11.200000, rms=0.563 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 51 after 21 iterations, nbhd size=1, neg = 0 0251: dt=11.200000, rms=0.562 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 49 after 12 iterations, nbhd size=0, neg = 0 0252: dt=11.200000, rms=0.561 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 59 after 11 iterations, nbhd size=0, neg = 0 0253: dt=11.200000, rms=0.560 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 86 after 7 iterations, nbhd size=0, neg = 0 0254: dt=11.200000, rms=0.559 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 102 after 16 iterations, nbhd size=1, neg = 0 0255: dt=11.200000, rms=0.558 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 105 after 11 iterations, nbhd size=0, neg = 0 0256: dt=11.200000, rms=0.557 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 100 after 9 iterations, nbhd size=0, neg = 0 0257: dt=11.200000, rms=0.556 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 110 after 19 iterations, nbhd size=1, neg = 0 0258: dt=11.200000, rms=0.555 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 175 after 13 iterations, nbhd size=0, neg = 0 0259: dt=11.200000, rms=0.555 (-0.013%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0260: dt=4.800000, rms=0.555 (0.002%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0261: dt=6.400000, rms=0.555 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.566, neg=0, invalid=762 iter 0, gcam->neg = 22 after 11 iterations, nbhd size=0, neg = 0 0262: dt=4.340426, rms=0.564 (0.403%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=0, neg = 0 0263: dt=1.728000, rms=0.564 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0264: dt=1.728000, rms=0.563 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 11 iterations, nbhd size=0, neg = 0 0265: dt=1.728000, rms=0.563 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=0, neg = 0 0266: dt=6.580645, rms=0.562 (0.477%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 11 iterations, nbhd size=0, neg = 0 0267: dt=9.580247, rms=0.561 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 5 iterations, nbhd size=0, neg = 0 0268: dt=9.580247, rms=0.561 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 5 iterations, nbhd size=0, neg = 0 0269: dt=9.580247, rms=0.559 (0.254%), neg=0, invalid=762 iter 0, gcam->neg = 51 after 14 iterations, nbhd size=0, neg = 0 0270: dt=9.580247, rms=0.558 (0.235%), neg=0, invalid=762 iter 0, gcam->neg = 99 after 18 iterations, nbhd size=1, neg = 0 0271: dt=9.580247, rms=0.556 (0.278%), neg=0, invalid=762 iter 0, gcam->neg = 145 after 22 iterations, nbhd size=1, neg = 0 0272: dt=9.580247, rms=0.553 (0.500%), neg=0, invalid=762 iter 0, gcam->neg = 201 after 9 iterations, nbhd size=0, neg = 0 0273: dt=9.580247, rms=0.550 (0.608%), neg=0, invalid=762 iter 0, gcam->neg = 187 after 16 iterations, nbhd size=0, neg = 0 0274: dt=9.580247, rms=0.548 (0.416%), neg=0, invalid=762 iter 0, gcam->neg = 194 after 28 iterations, nbhd size=1, neg = 0 0275: dt=9.580247, rms=0.548 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 185 after 11 iterations, nbhd size=0, neg = 0 0276: dt=9.580247, rms=0.548 (-0.106%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0277: dt=4.032000, rms=0.547 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0278: dt=4.032000, rms=0.547 (0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0279: dt=0.000000, rms=0.557 (0.229%), neg=0, invalid=762 0280: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0281: dt=0.000000, rms=0.557 (0.229%), neg=0, invalid=762 0282: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 iter 0, gcam->neg = 1493 after 19 iterations, nbhd size=1, neg = 0 0283: dt=1.453943, rms=0.521 (3.873%), neg=0, invalid=762 0284: dt=0.000013, rms=0.521 (-0.002%), neg=0, invalid=762 0285: dt=0.000013, rms=0.521 (0.000%), neg=0, invalid=762 0286: dt=0.000013, rms=0.521 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=762 0287: dt=0.112000, rms=0.521 (0.372%), neg=0, invalid=762 0288: dt=0.080000, rms=0.521 (0.030%), neg=0, invalid=762 0289: dt=0.080000, rms=0.521 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0290: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0291: dt=8.092000, rms=0.515 (0.001%), neg=0, invalid=762 0292: dt=6.936000, rms=0.515 (0.000%), neg=0, invalid=762 0293: dt=6.936000, rms=0.515 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0294: dt=2.268000, rms=0.515 (0.003%), neg=0, invalid=762 0295: dt=1.296000, rms=0.515 (0.000%), neg=0, invalid=762 0296: dt=1.296000, rms=0.515 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0297: dt=25.920000, rms=0.514 (0.035%), neg=0, invalid=762 0298: dt=36.288000, rms=0.514 (0.022%), neg=0, invalid=762 0299: dt=36.288000, rms=0.514 (0.021%), neg=0, invalid=762 0300: dt=36.288000, rms=0.514 (0.015%), neg=0, invalid=762 0301: dt=36.288000, rms=0.514 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0302: dt=6.400000, rms=0.514 (0.101%), neg=0, invalid=762 0303: dt=1.600000, rms=0.514 (0.004%), neg=0, invalid=762 0304: dt=1.600000, rms=0.514 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 iter 0, gcam->neg = 17 after 5 iterations, nbhd size=0, neg = 0 0305: dt=44.800000, rms=0.511 (0.569%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0306: dt=11.200000, rms=0.510 (0.172%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0307: dt=11.200000, rms=0.510 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0308: dt=11.200000, rms=0.510 (0.036%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=0, neg = 0 0309: dt=11.200000, rms=0.510 (0.036%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 17 iterations, nbhd size=1, neg = 0 0310: dt=38.400000, rms=0.509 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 6 iterations, nbhd size=0, neg = 0 0311: dt=44.800000, rms=0.509 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0312: dt=25.600000, rms=0.508 (0.082%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 iter 0, gcam->neg = 20 after 3 iterations, nbhd size=0, neg = 0 0313: dt=4.081633, rms=0.510 (0.145%), neg=0, invalid=762 0314: dt=0.252000, rms=0.510 (0.001%), neg=0, invalid=762 0315: dt=0.252000, rms=0.510 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0316: dt=0.252000, rms=0.510 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 iter 0, gcam->neg = 40 after 19 iterations, nbhd size=1, neg = 0 0317: dt=19.386243, rms=0.506 (0.743%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 6 iterations, nbhd size=0, neg = 0 0318: dt=13.358491, rms=0.504 (0.433%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=0, neg = 0 0319: dt=7.914894, rms=0.503 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 18 iterations, nbhd size=1, neg = 0 0320: dt=7.914894, rms=0.503 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 57 after 14 iterations, nbhd size=0, neg = 0 0321: dt=7.914894, rms=0.502 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 90 after 26 iterations, nbhd size=1, neg = 0 0322: dt=7.914894, rms=0.502 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 112 after 30 iterations, nbhd size=2, neg = 0 0323: dt=7.914894, rms=0.502 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.507, neg=0, invalid=762 0324: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.507, neg=0, invalid=762 0325: dt=0.000060, rms=0.507 (0.000%), neg=0, invalid=762 0326: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 iter 0, gcam->neg = 961 after 21 iterations, nbhd size=1, neg = 0 0327: dt=0.931931, rms=0.491 (1.534%), neg=0, invalid=762 0328: dt=0.000027, rms=0.491 (0.000%), neg=0, invalid=762 0329: dt=0.000027, rms=0.491 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 iter 0, gcam->neg = 33 after 3 iterations, nbhd size=0, neg = 0 0330: dt=0.448000, rms=0.488 (0.581%), neg=0, invalid=762 iter 0, gcam->neg = 266 after 14 iterations, nbhd size=1, neg = 0 0331: dt=0.650407, rms=0.486 (0.529%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0332: dt=0.256000, rms=0.485 (0.132%), neg=0, invalid=762 0333: dt=0.256000, rms=0.484 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0334: dt=0.256000, rms=0.483 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 5 iterations, nbhd size=0, neg = 0 0335: dt=0.256000, rms=0.482 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 38 after 16 iterations, nbhd size=1, neg = 0 0336: dt=0.256000, rms=0.482 (-0.002%), neg=0, invalid=762 0337: dt=0.112000, rms=0.482 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 39 after 15 iterations, nbhd size=1, neg = 0 0338: dt=0.448000, rms=0.482 (-0.031%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 44 minutes and 43 seconds. mri_ca_register utimesec 7794.139174 mri_ca_register stimesec 21.939837 mri_ca_register ru_maxrss 1350220 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 24893228 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 65160 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 37139 mri_ca_register ru_nivcsw 681506 FSRUNTIME@ mri_ca_register 1.7452 hours 4 threads #-------------------------------------- #@# SubCort Seg Fri Mar 31 14:10:39 CEST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname picasso machine x86_64 setenv SUBJECTS_DIR /net/analyse/eirik/fs6/subjects cd /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.86 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.07889 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (436 voxels, overlap=0.934) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (436 voxels, peak = 20), gca=20.5 gca peak = 0.17677 (13) mri peak = 0.07181 (16) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (276 voxels, overlap=0.755) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (276 voxels, peak = 15), gca=15.4 gca peak = 0.28129 (95) mri peak = 0.06557 (90) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (152 voxels, overlap=1.030) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (152 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.06558 (99) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (118 voxels, overlap=0.610) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (118 voxels, peak = 92), gca=91.7 gca peak = 0.24553 (55) mri peak = 0.08015 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (374 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (374 voxels, peak = 55), gca=55.0 gca peak = 0.30264 (59) mri peak = 0.07458 (50) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (395 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (395 voxels, peak = 57), gca=56.9 gca peak = 0.07580 (103) mri peak = 0.05845 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33007 voxels, overlap=0.891) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33007 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.06279 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37810 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37810 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.03547 (65) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29535 voxels, overlap=0.913) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29535 voxels, peak = 64), gca=63.5 gca peak = 0.11620 (58) mri peak = 0.03379 (56) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (26156 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (26156 voxels, peak = 56), gca=56.0 gca peak = 0.30970 (66) mri peak = 0.08014 (71) Right_Caudate (50): linear fit = 1.07 x + 0.0 (887 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.07 x + 0.0 (887 voxels, peak = 70), gca=70.3 gca peak = 0.15280 (69) mri peak = 0.07363 (75) Left_Caudate (11): linear fit = 1.00 x + 0.0 (918 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.00 x + 0.0 (918 voxels, peak = 69), gca=69.0 gca peak = 0.13902 (56) mri peak = 0.02576 (64) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (40515 voxels, overlap=0.013) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (40515 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.02471 (50) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (32171 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (32171 voxels, peak = 64), gca=63.5 gca peak = 0.16765 (84) mri peak = 0.05738 (82) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (6375 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (6375 voxels, peak = 83), gca=82.7 gca peak = 0.18739 (84) mri peak = 0.04229 (79) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (3696 voxels, overlap=0.857) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (3696 voxels, peak = 81), gca=81.1 gca peak = 0.29869 (57) mri peak = 0.11553 (74) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (93 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (93 voxels, peak = 72), gca=71.5 gca peak = 0.33601 (57) mri peak = 0.08165 (63) Right_Amygdala (54): linear fit = 1.09 x + 0.0 (69 voxels, overlap=0.358) Right_Amygdala (54): linear fit = 1.09 x + 0.0 (69 voxels, peak = 62), gca=61.8 gca peak = 0.11131 (90) mri peak = 0.07252 (83) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2832 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2832 voxels, peak = 87), gca=86.8 gca peak = 0.11793 (83) mri peak = 0.09150 (80) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (2583 voxels, overlap=0.901) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (2583 voxels, peak = 81), gca=80.9 gca peak = 0.08324 (81) mri peak = 0.06787 (76) Left_Putamen (12): linear fit = 0.96 x + 0.0 (728 voxels, overlap=0.912) Left_Putamen (12): linear fit = 0.96 x + 0.0 (728 voxels, peak = 78), gca=78.2 gca peak = 0.10360 (77) mri peak = 0.06456 (74) Right_Putamen (51): linear fit = 1.01 x + 0.0 (828 voxels, overlap=0.996) Right_Putamen (51): linear fit = 1.01 x + 0.0 (828 voxels, peak = 78), gca=78.2 gca peak = 0.08424 (78) mri peak = 0.09901 (81) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9040 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9040 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.07394 (81) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (510 voxels, overlap=0.826) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (510 voxels, peak = 90), gca=90.3 gca peak = 0.14500 (87) mri peak = 0.06909 (91) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (511 voxels, overlap=0.815) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (511 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) mri peak = 0.08479 (12) Fourth_Ventricle (15): linear fit = 0.76 x + 0.0 (374 voxels, overlap=0.641) Fourth_Ventricle (15): linear fit = 0.76 x + 0.0 (374 voxels, peak = 11), gca=10.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.06 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15138 (21) mri peak = 0.07889 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (436 voxels, overlap=0.932) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (436 voxels, peak = 22), gca=21.5 gca peak = 0.19455 (15) mri peak = 0.07181 (16) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (276 voxels, overlap=0.827) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (276 voxels, peak = 15), gca=15.4 gca peak = 0.27608 (88) mri peak = 0.06557 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (152 voxels, overlap=1.025) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (152 voxels, peak = 88), gca=87.6 gca peak = 0.19982 (92) mri peak = 0.06558 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (118 voxels, overlap=0.741) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (118 voxels, peak = 92), gca=91.5 gca peak = 0.24552 (55) mri peak = 0.08015 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (374 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (374 voxels, peak = 55), gca=55.0 gca peak = 0.31445 (57) mri peak = 0.07458 (50) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (395 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (395 voxels, peak = 57), gca=57.0 gca peak = 0.07767 (104) mri peak = 0.05845 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33007 voxels, overlap=0.921) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33007 voxels, peak = 104), gca=104.0 gca peak = 0.07714 (104) mri peak = 0.06279 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37810 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37810 voxels, peak = 104), gca=104.0 gca peak = 0.08766 (63) mri peak = 0.03547 (65) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29535 voxels, overlap=0.939) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29535 voxels, peak = 62), gca=62.1 gca peak = 0.11967 (56) mri peak = 0.03379 (56) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (26156 voxels, overlap=1.000) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (26156 voxels, peak = 59), gca=58.5 gca peak = 0.26033 (71) mri peak = 0.08014 (71) Right_Caudate (50): linear fit = 1.00 x + 0.0 (887 voxels, overlap=1.010) Right_Caudate (50): linear fit = 1.00 x + 0.0 (887 voxels, peak = 71), gca=71.0 gca peak = 0.15150 (69) mri peak = 0.07363 (75) Left_Caudate (11): linear fit = 1.00 x + 0.0 (918 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.00 x + 0.0 (918 voxels, peak = 69), gca=69.0 gca peak = 0.12636 (63) mri peak = 0.02576 (64) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (40515 voxels, overlap=0.248) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (40515 voxels, peak = 62), gca=62.1 gca peak = 0.12837 (63) mri peak = 0.02471 (50) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32171 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32171 voxels, peak = 62), gca=62.1 gca peak = 0.16115 (83) mri peak = 0.05738 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6375 voxels, overlap=0.975) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6375 voxels, peak = 83), gca=82.6 gca peak = 0.17629 (81) mri peak = 0.04229 (79) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3696 voxels, overlap=0.971) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3696 voxels, peak = 81), gca=80.6 gca peak = 0.23952 (73) mri peak = 0.11553 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (93 voxels, overlap=1.013) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (93 voxels, peak = 73), gca=73.0 gca peak = 0.32419 (62) mri peak = 0.08165 (63) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (69 voxels, overlap=0.987) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (69 voxels, peak = 62), gca=62.0 gca peak = 0.11101 (87) mri peak = 0.07252 (83) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (2832 voxels, overlap=0.972) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (2832 voxels, peak = 86), gca=85.7 gca peak = 0.11482 (79) mri peak = 0.09150 (80) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2583 voxels, overlap=0.904) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2583 voxels, peak = 79), gca=78.6 gca peak = 0.08891 (78) mri peak = 0.06787 (76) Left_Putamen (12): linear fit = 1.01 x + 0.0 (728 voxels, overlap=0.870) Left_Putamen (12): linear fit = 1.01 x + 0.0 (728 voxels, peak = 79), gca=79.2 gca peak = 0.08217 (78) mri peak = 0.06456 (74) Right_Putamen (51): linear fit = 0.99 x + 0.0 (828 voxels, overlap=0.991) Right_Putamen (51): linear fit = 0.99 x + 0.0 (828 voxels, peak = 77), gca=76.8 gca peak = 0.06970 (83) mri peak = 0.09901 (81) Brain_Stem (16): linear fit = 0.99 x + 0.0 (9040 voxels, overlap=0.700) Brain_Stem (16): linear fit = 0.99 x + 0.0 (9040 voxels, peak = 82), gca=81.8 gca peak = 0.12238 (89) mri peak = 0.07394 (81) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (510 voxels, overlap=0.825) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (510 voxels, peak = 89), gca=88.6 gca peak = 0.16544 (91) mri peak = 0.06909 (91) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (511 voxels, overlap=0.743) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (511 voxels, peak = 90), gca=89.6 gca peak = 0.13735 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.23403 (11) mri peak = 0.08479 (12) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (374 voxels, overlap=0.865) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (374 voxels, peak = 11), gca=11.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17808 (26) gca peak Left_Thalamus = 1.00000 (100) gca peak Third_Ventricle = 0.13735 (23) gca peak CSF = 0.28459 (36) gca peak Left_Accumbens_area = 0.61385 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.76046 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.31943 (69) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.54107 (32) gca peak WM_hypointensities = 0.07991 (77) gca peak non_WM_hypointensities = 0.09318 (44) gca peak Optic_Chiasm = 0.71105 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.03 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 150253 voxels changed in iteration 0 of unlikely voxel relabeling 292 voxels changed in iteration 1 of unlikely voxel relabeling 14 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 70773 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 803 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 116778 changed. image ll: -2.290, PF=0.500 pass 2: 40353 changed. image ll: -2.289, PF=0.500 pass 3: 15203 changed. pass 4: 6990 changed. pass 5: 3424 changed. 102991 voxels changed in iteration 0 of unlikely voxel relabeling 629 voxels changed in iteration 1 of unlikely voxel relabeling 17 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 10601 voxels changed in iteration 0 of unlikely voxel relabeling 77 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9482 voxels changed in iteration 0 of unlikely voxel relabeling 110 voxels changed in iteration 1 of unlikely voxel relabeling 18 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8714 voxels changed in iteration 0 of unlikely voxel relabeling 54 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4301.469771 mri_ca_label stimesec 8.891907 mri_ca_label ru_maxrss 2103216 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 13229896 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 504 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 695 mri_ca_label ru_nivcsw 369941 auto-labeling took 70 minutes and 47 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/cc_up.lta top3T_0186.fs6.3T.T2pial will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/transforms/cc_up.lta reading aseg from /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/aseg.auto_noCCseg.mgz reading norm from /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/norm.mgz 44269 voxels in left wm, 75935 in right wm, xrange [120, 132] searching rotation angles z=[-9 5], y=[-10 4] searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 global minimum found at slice 127.2, rotations (-2.61, -2.45) final transformation (x=127.2, yr=-2.615, zr=-2.454): 0.99804 0.04281 -0.04558 3.11842; -0.04277 0.99908 0.00195 70.29379; 0.04562 0.00000 0.99896 17.30592; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 63 105 eigenvectors: 0.00158 -0.00401 0.99999; -0.19913 -0.97997 -0.00362; 0.97997 -0.19912 -0.00234; writing aseg with callosum to /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri/aseg.auto.mgz... corpus callosum segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Fri Mar 31 15:22:29 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Mar 31 15:22:29 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1866 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 103 gm peak at 66 (66), valley at 18 (18) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 66 (66), valley at 17 (17) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 14 seconds. #-------------------------------------------- #@# Mask BFS Fri Mar 31 15:25:44 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1691070 voxels in mask (pct= 10.08) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Mar 31 15:25:45 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.4 +- 5.9 [79.0 --> 125.0] GM (68.0) : 66.1 +- 10.6 [30.0 --> 95.0] setting bottom of white matter range to 76.7 setting top of gray matter range to 87.3 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 17510 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3704 filled 5036 bright non-wm voxels segmented. 9386 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.84 minutes reading wm segmentation from wm.seg.mgz... 2387 voxels added to wm to prevent paths from MTL structures to cortex 5970 additional wm voxels added 0 additional wm voxels added SEG EDIT: 48138 voxels turned on, 44032 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 89 found - 89 modified | TOTAL: 89 pass 2 (xy+): 0 found - 89 modified | TOTAL: 89 pass 1 (xy-): 114 found - 114 modified | TOTAL: 203 pass 2 (xy-): 0 found - 114 modified | TOTAL: 203 pass 1 (yz+): 101 found - 101 modified | TOTAL: 304 pass 2 (yz+): 0 found - 101 modified | TOTAL: 304 pass 1 (yz-): 89 found - 89 modified | TOTAL: 393 pass 2 (yz-): 0 found - 89 modified | TOTAL: 393 pass 1 (xz+): 85 found - 85 modified | TOTAL: 478 pass 2 (xz+): 0 found - 85 modified | TOTAL: 478 pass 1 (xz-): 93 found - 93 modified | TOTAL: 571 pass 2 (xz-): 0 found - 93 modified | TOTAL: 571 Iteration Number : 1 pass 1 (+++): 149 found - 149 modified | TOTAL: 149 pass 2 (+++): 0 found - 149 modified | TOTAL: 149 pass 1 (+++): 140 found - 140 modified | TOTAL: 289 pass 2 (+++): 0 found - 140 modified | TOTAL: 289 pass 1 (+++): 189 found - 189 modified | TOTAL: 478 pass 2 (+++): 0 found - 189 modified | TOTAL: 478 pass 1 (+++): 160 found - 160 modified | TOTAL: 638 pass 2 (+++): 0 found - 160 modified | TOTAL: 638 Iteration Number : 1 pass 1 (++): 344 found - 344 modified | TOTAL: 344 pass 2 (++): 0 found - 344 modified | TOTAL: 344 pass 1 (+-): 409 found - 409 modified | TOTAL: 753 pass 2 (+-): 0 found - 409 modified | TOTAL: 753 pass 1 (--): 417 found - 417 modified | TOTAL: 1170 pass 2 (--): 0 found - 417 modified | TOTAL: 1170 pass 1 (-+): 389 found - 389 modified | TOTAL: 1559 pass 2 (-+): 0 found - 389 modified | TOTAL: 1559 Iteration Number : 2 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 42 found - 42 modified | TOTAL: 70 pass 2 (xy-): 0 found - 42 modified | TOTAL: 70 pass 1 (yz+): 48 found - 48 modified | TOTAL: 118 pass 2 (yz+): 0 found - 48 modified | TOTAL: 118 pass 1 (yz-): 50 found - 50 modified | TOTAL: 168 pass 2 (yz-): 0 found - 50 modified | TOTAL: 168 pass 1 (xz+): 42 found - 42 modified | TOTAL: 210 pass 2 (xz+): 0 found - 42 modified | TOTAL: 210 pass 1 (xz-): 47 found - 47 modified | TOTAL: 257 pass 2 (xz-): 0 found - 47 modified | TOTAL: 257 Iteration Number : 2 pass 1 (+++): 21 found - 21 modified | TOTAL: 21 pass 2 (+++): 0 found - 21 modified | TOTAL: 21 pass 1 (+++): 22 found - 22 modified | TOTAL: 43 pass 2 (+++): 0 found - 22 modified | TOTAL: 43 pass 1 (+++): 24 found - 24 modified | TOTAL: 67 pass 2 (+++): 0 found - 24 modified | TOTAL: 67 pass 1 (+++): 23 found - 23 modified | TOTAL: 90 pass 2 (+++): 0 found - 23 modified | TOTAL: 90 Iteration Number : 2 pass 1 (++): 24 found - 24 modified | TOTAL: 24 pass 2 (++): 0 found - 24 modified | TOTAL: 24 pass 1 (+-): 29 found - 29 modified | TOTAL: 53 pass 2 (+-): 0 found - 29 modified | TOTAL: 53 pass 1 (--): 19 found - 19 modified | TOTAL: 72 pass 2 (--): 0 found - 19 modified | TOTAL: 72 pass 1 (-+): 23 found - 23 modified | TOTAL: 95 pass 2 (-+): 0 found - 23 modified | TOTAL: 95 Iteration Number : 3 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 2 found - 2 modified | TOTAL: 8 pass 2 (xy-): 0 found - 2 modified | TOTAL: 8 pass 1 (yz+): 8 found - 8 modified | TOTAL: 16 pass 2 (yz+): 0 found - 8 modified | TOTAL: 16 pass 1 (yz-): 8 found - 8 modified | TOTAL: 24 pass 2 (yz-): 0 found - 8 modified | TOTAL: 24 pass 1 (xz+): 7 found - 7 modified | TOTAL: 31 pass 2 (xz+): 0 found - 7 modified | TOTAL: 31 pass 1 (xz-): 11 found - 11 modified | TOTAL: 42 pass 2 (xz-): 0 found - 11 modified | TOTAL: 42 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 4 found - 4 modified | TOTAL: 4 pass 2 (+-): 0 found - 4 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 4 found - 4 modified | TOTAL: 11 pass 2 (-+): 0 found - 4 modified | TOTAL: 11 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3277 (out of 529816: 0.618517) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Mar 31 15:28:20 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.99422 0.02400 -0.09370 5.70293; -0.00135 1.00751 0.24436 7.31068; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.99422 0.02400 -0.09370 5.70293; -0.00135 1.00751 0.24436 7.31068; 0.09747 -0.22904 0.95041 16.14852; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1510 (min = 350, max = 1400), aspect = 0.86 (min = 0.10, max = 0.75) need search nearby using seed (122, 116, 146), TAL = (6.0, 18.0, 12.0) talairach voxel to voxel transform 0.99615 -0.00133 0.09855 -7.26270; 0.02467 0.93770 -0.23866 -3.14187; -0.09622 0.22611 0.98456 -17.00345; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (122, 116, 146) --> (6.0, 18.0, 12.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (6.00, 18.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(24.00, 18.00, 12.00) SRC: (110.57, 73.35, 142.96) search lh wm seed point around talairach space (-12.00, 18.00, 12.00), SRC: (146.43, 74.24, 139.50) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Mar 31 15:29:03 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 4 found - 4 modified | TOTAL: 16 pass 2 (xz+): 0 found - 4 modified | TOTAL: 16 pass 1 (xz-): 1 found - 1 modified | TOTAL: 17 pass 2 (xz-): 0 found - 1 modified | TOTAL: 17 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 2 found - 2 modified | TOTAL: 5 pass 2 (+-): 0 found - 2 modified | TOTAL: 5 pass 1 (--): 3 found - 3 modified | TOTAL: 8 pass 2 (--): 0 found - 3 modified | TOTAL: 8 pass 1 (-+): 1 found - 1 modified | TOTAL: 9 pass 2 (-+): 0 found - 1 modified | TOTAL: 9 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 26 (out of 269467: 0.009649) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 95 vertices, 111 faces slice 40: 3442 vertices, 3678 faces slice 50: 12654 vertices, 13067 faces slice 60: 25890 vertices, 26445 faces slice 70: 39431 vertices, 39919 faces slice 80: 52940 vertices, 53524 faces slice 90: 67825 vertices, 68469 faces slice 100: 84047 vertices, 84811 faces slice 110: 100331 vertices, 101111 faces slice 120: 118004 vertices, 118942 faces slice 130: 133045 vertices, 134003 faces slice 140: 146815 vertices, 147808 faces slice 150: 159536 vertices, 160570 faces slice 160: 171612 vertices, 172570 faces slice 170: 181308 vertices, 182339 faces slice 180: 189035 vertices, 189960 faces slice 190: 192112 vertices, 192895 faces slice 200: 192362 vertices, 193108 faces slice 210: 192362 vertices, 193108 faces slice 220: 192362 vertices, 193108 faces slice 230: 192362 vertices, 193108 faces slice 240: 192362 vertices, 193108 faces slice 250: 192362 vertices, 193108 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 192362 voxel in cpt #1: X=-746 [v=192362,e=579324,f=386216] located at (-29.431000, -21.236113, 50.933437) For the whole surface: X=-746 [v=192362,e=579324,f=386216] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Mar 31 15:29:09 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 7 found - 7 modified | TOTAL: 11 pass 2 (yz-): 0 found - 7 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 17 (out of 251342: 0.006764) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 3766 vertices, 4009 faces slice 50: 14257 vertices, 14683 faces slice 60: 27277 vertices, 27791 faces slice 70: 40520 vertices, 41000 faces slice 80: 54543 vertices, 55022 faces slice 90: 69109 vertices, 69681 faces slice 100: 82569 vertices, 83182 faces slice 110: 96673 vertices, 97398 faces slice 120: 111833 vertices, 112609 faces slice 130: 124675 vertices, 125417 faces slice 140: 136516 vertices, 137290 faces slice 150: 148468 vertices, 149312 faces slice 160: 158185 vertices, 158979 faces slice 170: 166629 vertices, 167452 faces slice 180: 172441 vertices, 173139 faces slice 190: 173656 vertices, 174254 faces slice 200: 173656 vertices, 174254 faces slice 210: 173656 vertices, 174254 faces slice 220: 173656 vertices, 174254 faces slice 230: 173656 vertices, 174254 faces slice 240: 173656 vertices, 174254 faces slice 250: 173656 vertices, 174254 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 173656 voxel in cpt #1: X=-598 [v=173656,e=522762,f=348508] located at (30.343069, -25.048929, 53.792545) For the whole surface: X=-598 [v=173656,e=522762,f=348508] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Mar 31 15:29:15 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Mar 31 15:29:15 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 19192 of (19192 19195) to complete... Waiting for PID 19195 of (19192 19195) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (19192 19195) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Mar 31 15:29:24 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Mar 31 15:29:24 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 19245 of (19245 19248) to complete... Waiting for PID 19248 of (19245 19248) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.3 mm, total surface area = 93437 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.200 (target=0.015) step 005: RMS=0.159 (target=0.015) step 010: RMS=0.136 (target=0.015) step 015: RMS=0.127 (target=0.015) step 020: RMS=0.121 (target=0.015) step 025: RMS=0.117 (target=0.015) step 030: RMS=0.114 (target=0.015) step 035: RMS=0.111 (target=0.015) step 040: RMS=0.110 (target=0.015) step 045: RMS=0.109 (target=0.015) step 050: RMS=0.108 (target=0.015) step 055: RMS=0.108 (target=0.015) step 060: RMS=0.108 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 67.400325 mris_inflate stimesec 0.687146 mris_inflate ru_maxrss 300188 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 283720 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13584 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 75513 mris_inflate ru_nivcsw 7016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 85212 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.198 (target=0.015) step 005: RMS=0.156 (target=0.015) step 010: RMS=0.132 (target=0.015) step 015: RMS=0.123 (target=0.015) step 020: RMS=0.117 (target=0.015) step 025: RMS=0.111 (target=0.015) step 030: RMS=0.109 (target=0.015) step 035: RMS=0.107 (target=0.015) step 040: RMS=0.105 (target=0.015) step 045: RMS=0.104 (target=0.015) step 050: RMS=0.102 (target=0.015) step 055: RMS=0.103 (target=0.015) step 060: RMS=0.103 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 73.034662 mris_inflate stimesec 1.076619 mris_inflate ru_maxrss 270752 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 394366 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12264 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 81535 mris_inflate ru_nivcsw 7568 PIDs (19245 19248) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Mar 31 15:29:52 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Mar 31 15:29:52 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 19309 of (19309 19312) to complete... Waiting for PID 19312 of (19309 19312) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.65 (0.00-->12.49) (max @ vno 113377 --> 113396) face area 0.02 +- 0.04 (-0.50-->0.77) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.019, avgs=0 005/300: dt: 0.9000, rms radial error=176.762, avgs=0 010/300: dt: 0.9000, rms radial error=176.204, avgs=0 015/300: dt: 0.9000, rms radial error=175.469, avgs=0 020/300: dt: 0.9000, rms radial error=174.632, avgs=0 025/300: dt: 0.9000, rms radial error=173.738, avgs=0 030/300: dt: 0.9000, rms radial error=172.812, avgs=0 035/300: dt: 0.9000, rms radial error=171.869, avgs=0 040/300: dt: 0.9000, rms radial error=170.918, avgs=0 045/300: dt: 0.9000, rms radial error=169.965, avgs=0 050/300: dt: 0.9000, rms radial error=169.012, avgs=0 055/300: dt: 0.9000, rms radial error=168.062, avgs=0 060/300: dt: 0.9000, rms radial error=167.121, avgs=0 065/300: dt: 0.9000, rms radial error=166.188, avgs=0 070/300: dt: 0.9000, rms radial error=165.261, avgs=0 075/300: dt: 0.9000, rms radial error=164.338, avgs=0 080/300: dt: 0.9000, rms radial error=163.420, avgs=0 085/300: dt: 0.9000, rms radial error=162.508, avgs=0 090/300: dt: 0.9000, rms radial error=161.599, avgs=0 095/300: dt: 0.9000, rms radial error=160.696, avgs=0 100/300: dt: 0.9000, rms radial error=159.798, avgs=0 105/300: dt: 0.9000, rms radial error=158.905, avgs=0 110/300: dt: 0.9000, rms radial error=158.017, avgs=0 115/300: dt: 0.9000, rms radial error=157.133, avgs=0 120/300: dt: 0.9000, rms radial error=156.255, avgs=0 125/300: dt: 0.9000, rms radial error=155.381, avgs=0 130/300: dt: 0.9000, rms radial error=154.512, avgs=0 135/300: dt: 0.9000, rms radial error=153.648, avgs=0 140/300: dt: 0.9000, rms radial error=152.788, avgs=0 145/300: dt: 0.9000, rms radial error=151.933, avgs=0 150/300: dt: 0.9000, rms radial error=151.084, avgs=0 155/300: dt: 0.9000, rms radial error=150.239, avgs=0 160/300: dt: 0.9000, rms radial error=149.398, avgs=0 165/300: dt: 0.9000, rms radial error=148.563, avgs=0 170/300: dt: 0.9000, rms radial error=147.732, avgs=0 175/300: dt: 0.9000, rms radial error=146.906, avgs=0 180/300: dt: 0.9000, rms radial error=146.085, avgs=0 185/300: dt: 0.9000, rms radial error=145.268, avgs=0 190/300: dt: 0.9000, rms radial error=144.455, avgs=0 195/300: dt: 0.9000, rms radial error=143.648, avgs=0 200/300: dt: 0.9000, rms radial error=142.845, avgs=0 205/300: dt: 0.9000, rms radial error=142.046, avgs=0 210/300: dt: 0.9000, rms radial error=141.252, avgs=0 215/300: dt: 0.9000, rms radial error=140.462, avgs=0 220/300: dt: 0.9000, rms radial error=139.676, avgs=0 225/300: dt: 0.9000, rms radial error=138.894, avgs=0 230/300: dt: 0.9000, rms radial error=138.117, avgs=0 235/300: dt: 0.9000, rms radial error=137.345, avgs=0 240/300: dt: 0.9000, rms radial error=136.576, avgs=0 245/300: dt: 0.9000, rms radial error=135.812, avgs=0 250/300: dt: 0.9000, rms radial error=135.052, avgs=0 255/300: dt: 0.9000, rms radial error=134.297, avgs=0 260/300: dt: 0.9000, rms radial error=133.545, avgs=0 265/300: dt: 0.9000, rms radial error=132.798, avgs=0 270/300: dt: 0.9000, rms radial error=132.055, avgs=0 275/300: dt: 0.9000, rms radial error=131.316, avgs=0 280/300: dt: 0.9000, rms radial error=130.580, avgs=0 285/300: dt: 0.9000, rms radial error=129.849, avgs=0 290/300: dt: 0.9000, rms radial error=129.123, avgs=0 295/300: dt: 0.9000, rms radial error=128.400, avgs=0 300/300: dt: 0.9000, rms radial error=127.681, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23571.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 2 (K=40.0), pass 1, starting sse = 4600.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00070 epoch 3 (K=160.0), pass 1, starting sse = 815.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00599 epoch 4 (K=640.0), pass 1, starting sse = 212.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/14 = 0.01087 final distance error %32.63 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 443.733549 mris_sphere stimesec 1.362899 mris_sphere ru_maxrss 300420 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1032248 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13608 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 95050 mris_sphere ru_nivcsw 42378 FSRUNTIME@ mris_sphere 0.0508 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.62 (0.00-->9.58) (max @ vno 122850 --> 122859) face area 0.02 +- 0.03 (-0.20-->0.51) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.305... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.978, avgs=0 005/300: dt: 0.9000, rms radial error=175.722, avgs=0 010/300: dt: 0.9000, rms radial error=175.173, avgs=0 015/300: dt: 0.9000, rms radial error=174.451, avgs=0 020/300: dt: 0.9000, rms radial error=173.630, avgs=0 025/300: dt: 0.9000, rms radial error=172.752, avgs=0 030/300: dt: 0.9000, rms radial error=171.843, avgs=0 035/300: dt: 0.9000, rms radial error=170.912, avgs=0 040/300: dt: 0.9000, rms radial error=169.968, avgs=0 045/300: dt: 0.9000, rms radial error=169.022, avgs=0 050/300: dt: 0.9000, rms radial error=168.077, avgs=0 055/300: dt: 0.9000, rms radial error=167.135, avgs=0 060/300: dt: 0.9000, rms radial error=166.197, avgs=0 065/300: dt: 0.9000, rms radial error=165.263, avgs=0 070/300: dt: 0.9000, rms radial error=164.334, avgs=0 075/300: dt: 0.9000, rms radial error=163.411, avgs=0 080/300: dt: 0.9000, rms radial error=162.492, avgs=0 085/300: dt: 0.9000, rms radial error=161.579, avgs=0 090/300: dt: 0.9000, rms radial error=160.671, avgs=0 095/300: dt: 0.9000, rms radial error=159.767, avgs=0 100/300: dt: 0.9000, rms radial error=158.869, avgs=0 105/300: dt: 0.9000, rms radial error=157.976, avgs=0 110/300: dt: 0.9000, rms radial error=157.088, avgs=0 115/300: dt: 0.9000, rms radial error=156.205, avgs=0 120/300: dt: 0.9000, rms radial error=155.327, avgs=0 125/300: dt: 0.9000, rms radial error=154.453, avgs=0 130/300: dt: 0.9000, rms radial error=153.586, avgs=0 135/300: dt: 0.9000, rms radial error=152.723, avgs=0 140/300: dt: 0.9000, rms radial error=151.865, avgs=0 145/300: dt: 0.9000, rms radial error=151.012, avgs=0 150/300: dt: 0.9000, rms radial error=150.164, avgs=0 155/300: dt: 0.9000, rms radial error=149.320, avgs=0 160/300: dt: 0.9000, rms radial error=148.482, avgs=0 165/300: dt: 0.9000, rms radial error=147.648, avgs=0 170/300: dt: 0.9000, rms radial error=146.820, avgs=0 175/300: dt: 0.9000, rms radial error=145.995, avgs=0 180/300: dt: 0.9000, rms radial error=145.176, avgs=0 185/300: dt: 0.9000, rms radial error=144.361, avgs=0 190/300: dt: 0.9000, rms radial error=143.551, avgs=0 195/300: dt: 0.9000, rms radial error=142.745, avgs=0 200/300: dt: 0.9000, rms radial error=141.943, avgs=0 205/300: dt: 0.9000, rms radial error=141.146, avgs=0 210/300: dt: 0.9000, rms radial error=140.353, avgs=0 215/300: dt: 0.9000, rms radial error=139.566, avgs=0 220/300: dt: 0.9000, rms radial error=138.783, avgs=0 225/300: dt: 0.9000, rms radial error=138.004, avgs=0 230/300: dt: 0.9000, rms radial error=137.230, avgs=0 235/300: dt: 0.9000, rms radial error=136.460, avgs=0 240/300: dt: 0.9000, rms radial error=135.694, avgs=0 245/300: dt: 0.9000, rms radial error=134.933, avgs=0 250/300: dt: 0.9000, rms radial error=134.176, avgs=0 255/300: dt: 0.9000, rms radial error=133.423, avgs=0 260/300: dt: 0.9000, rms radial error=132.674, avgs=0 265/300: dt: 0.9000, rms radial error=131.930, avgs=0 270/300: dt: 0.9000, rms radial error=131.190, avgs=0 275/300: dt: 0.9000, rms radial error=130.453, avgs=0 280/300: dt: 0.9000, rms radial error=129.722, avgs=0 285/300: dt: 0.9000, rms radial error=128.994, avgs=0 290/300: dt: 0.9000, rms radial error=128.270, avgs=0 295/300: dt: 0.9000, rms radial error=127.551, avgs=0 300/300: dt: 0.9000, rms radial error=126.835, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20875.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3865.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00024 epoch 3 (K=160.0), pass 1, starting sse = 581.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00240 epoch 4 (K=640.0), pass 1, starting sse = 102.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00511 final distance error %29.86 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 345.324616 mris_sphere stimesec 0.842829 mris_sphere ru_maxrss 270988 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 425462 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12288 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 81720 mris_sphere ru_nivcsw 32635 FSRUNTIME@ mris_sphere 0.0390 hours 1 threads PIDs (19309 19312) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Fri Mar 31 15:32:55 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri Mar 31 15:32:55 CEST 2017 /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri Mar 31 15:32:55 CEST 2017 mris_fix_topology -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 top3T_0186.fs6.3T.T2pial lh #@# Fix Topology rh Fri Mar 31 15:32:55 CEST 2017 mris_fix_topology -rusage /net/analyse/eirik/fs6/subjects/top3T_0186.fs6.3T.T2pial/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 top3T_0186.fs6.3T.T2pial rh Waiting for PID 19701 of (19701 19704) to complete...