Thu Mar 1 01:58:34 UTC 2018 /usr/local/freesurfer/subjects/matt2 /usr/local/freesurfer/bin/recon-all -s matt2 -i /home/matt/freesurfer/subjects/mattmri2/IM000001 -all subjid matt2 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 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 4096 maxlocks unlimited maxsignal 65506 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16783224 268096 16387096 8456 128032 16262876 Swap: 0 0 0 ######################################## 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: 2018/03/01-01:58:35-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2018/03/01-01:58:35-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:36-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:37-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:38-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2018/03/01-01:58:39-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/01-01:58:40-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: matt Machine: centos-7-1 Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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 ####################################### /usr/local/freesurfer/subjects/matt2 mri_convert /home/matt/freesurfer/subjects/mattmri2/IM000001 /usr/local/freesurfer/subjects/matt2/mri/orig/001.mgz mri_convert.bin /home/matt/freesurfer/subjects/mattmri2/IM000001 /usr/local/freesurfer/subjects/matt2/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/matt/freesurfer/subjects/mattmri2/IM000001... Getting Series No INFO: Found 811 files in /home/matt/freesurfer/subjects/mattmri2 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 42 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (320 320 42), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /home/matt/freesurfer/subjects/mattmri2/IM000042 Identification NumarisVer syngo MR E11 ScannerModel Skyra PatientName GRECSEK^MATTHEW^THOMAS Date and time StudyDate 20171221 StudyTime 073750.039000 SeriesTime 074125.770000 AcqTime 074123.557500 Acquisition parameters PulseSeq *tseB2d1_18 Protocol SAG TSE T2 PhEncDir ROW EchoNo 1 FlipAngle 146 EchoTime 90 InversionTime -1 RepetitionTime 4000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 42 NImageRows 320 NImageCols 320 NFrames 1 SliceArraylSize 42 IsMosaic 0 ImgPos 71.2021 105.0703 89.3746 VolRes 0.7500 0.7500 3.5100 VolDim 320 320 42 Vc 0.0042 -0.9988 -0.0495 Vr -0.0258 0.0494 -0.9984 Vs -0.9997 -0.0055 0.0256 VolCenter -5.0697 -9.2597 -34.4980 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (0.00424928, -0.998764, -0.0495309) j_ras = (-0.0258081, 0.0494053, -0.998445) k_ras = (-0.999658, -0.005521, 0.0255663) writing to /usr/local/freesurfer/subjects/matt2/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Mar 1 01:58:50 UTC 2018 Found 1 runs /usr/local/freesurfer/subjects/matt2/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 /usr/local/freesurfer/subjects/matt2/mri/orig/001.mgz /usr/local/freesurfer/subjects/matt2/mri/rawavg.mgz /usr/local/freesurfer/subjects/matt2 mri_convert /usr/local/freesurfer/subjects/matt2/mri/rawavg.mgz /usr/local/freesurfer/subjects/matt2/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/matt2/mri/rawavg.mgz /usr/local/freesurfer/subjects/matt2/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/matt2/mri/rawavg.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (0.00424928, -0.998764, -0.0495309) j_ras = (-0.0258081, 0.0494053, -0.998445) k_ras = (-0.999658, -0.005521, 0.0255663) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/matt2/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/matt2/mri/orig.mgz /usr/local/freesurfer/subjects/matt2/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 1 01:58:57 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/matt2/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 centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 1 01:58:57 UTC 2018 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.1411 /usr/local/freesurfer/subjects/matt2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1411/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1411/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1411/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 1 01:58:59 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.1411/nu0.mnc ./tmp.mri_nu_correct.mni.1411/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1411/0/ -iterations 1000 -distance 50 [matt@centos-7-1:/usr/local/freesurfer/subjects/matt2/mri/] [2018-03-01 01:59:00] 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.1411/0/ ./tmp.mri_nu_correct.mni.1411/nu0.mnc ./tmp.mri_nu_correct.mni.1411/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 24 CV of field change: 0.000986077 mri_convert ./tmp.mri_nu_correct.mni.1411/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.1411/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1411/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) 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... Thu Mar 1 01:59:50 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Mar 1 01:59:50 UTC 2018 Ended at Thu Mar 1 02:00:21 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Mar 1 02:00:23 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2023, pval=0.0127 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach_avi.log TalAviQA: 0.90027 z-score: -17 WARNING: Talairach QA check failed! z-score of -17 is <= threshold of -9 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Retrying Talairach align using 3T-based atlas... #-------------------------------------------- #@# Talairach Thu Mar 1 02:00:23 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/matt2/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 centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 1 02:00:23 UTC 2018 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.1958 /usr/local/freesurfer/subjects/matt2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1958/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1958/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1958/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 1 02:00:25 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.1958/nu0.mnc ./tmp.mri_nu_correct.mni.1958/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1958/0/ -iterations 1000 -distance 50 [matt@centos-7-1:/usr/local/freesurfer/subjects/matt2/mri/] [2018-03-01 02:00:25] 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.1958/0/ ./tmp.mri_nu_correct.mni.1958/nu0.mnc ./tmp.mri_nu_correct.mni.1958/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 24 CV of field change: 0.000986077 mri_convert ./tmp.mri_nu_correct.mni.1958/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.1958/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1958/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) 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... Thu Mar 1 02:01:15 UTC 2018 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 Thu Mar 1 02:01:15 UTC 2018 Ended at Thu Mar 1 02:01:44 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Mar 1 02:01:46 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5822, pval=0.2817 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach_avi.log TalAviQA: 0.87324 z-score: -23 WARNING: Talairach QA check failed! z-score of -23 is <= threshold of -9 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Thu Mar 1 02:01:46 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/matt2/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 centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 1 02:01:46 UTC 2018 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.2527 /usr/local/freesurfer/subjects/matt2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2527/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2527/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2527/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 1 02:01:48 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.2527/nu0.mnc ./tmp.mri_nu_correct.mni.2527/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2527/0/ -iterations 1000 -distance 50 [matt@centos-7-1:/usr/local/freesurfer/subjects/matt2/mri/] [2018-03-01 02:01:48] 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.2527/0/ ./tmp.mri_nu_correct.mni.2527/nu0.mnc ./tmp.mri_nu_correct.mni.2527/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 24 CV of field change: 0.000986077 mri_convert ./tmp.mri_nu_correct.mni.2527/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.2527/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.2527/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) 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... Thu Mar 1 02:02:38 UTC 2018 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/matt2/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $ Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 1 02:02:38 UTC 2018 tmpdir is transforms/tmp.talairach.2929 /usr/local/freesurfer/subjects/matt2/mri mri_convert orig_nu.mgz transforms/tmp.talairach.2929/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.2929/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) writing to transforms/tmp.talairach.2929/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.2929/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 178.221 Source min/max voxel= -0.000 178.221 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 3.1703 0.0000 1.0000 0.0000 -17.0353 0.0000 0.0000 1.0000 51.0046 Transform center = -2.842 -0.556 -41.550 Transform rotations = 0.000 0.000 0.000 Transform trans = 3.170 -17.035 51.005 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 227.453 Source min/max voxel= -0.000 227.453 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 1.0013 -0.0192 0.0192 3.1774 0.0136 0.9674 0.2596 -2.5941 -0.0235 -0.2592 0.9673 18.7966 Transform center = -2.842 -0.556 -41.550 Transform rotations = -0.262 0.023 0.014 Transform trans = 2.388 -13.400 20.367 Transform scale = 1.002 1.002 1.002 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.089 26.022 Source min/max voxel= 0.089 26.022 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 1.0427 0.0002 -0.0093 1.0423 0.0024 1.0003 0.2944 -5.4082 0.0090 -0.2944 1.0002 14.9104 Transform center = -2.842 -0.556 -41.550 Transform rotations = -0.286 -0.009 0.002 Transform trans = 1.308 -17.646 15.038 Transform scale = 1.043 1.043 1.043 Transform shear = 0.000 -0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.089 26.022 Source min/max voxel= 0.089 26.022 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.9352 -0.0185 -0.0648 1.4725 0.0433 0.8556 0.3810 7.6314 0.0516 -0.3830 0.8542 10.7683 Transform center = -2.842 -0.556 -41.550 Transform rotations = -0.422 -0.055 0.046 Transform trans = 4.360 -8.243 16.891 Transform scale = 0.938 0.938 0.938 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.089 26.022 Source min/max voxel= 0.089 26.022 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.9211 -0.0201 -0.0618 1.6424 0.0432 0.8794 0.3576 7.3629 0.0525 -0.3694 0.9020 11.4034 Transform center = -2.842 -0.556 -41.550 Transform rotations = -0.389 -0.054 0.046 Transform trans = 4.447 -7.553 15.532 Transform scale = 0.923 0.950 0.976 Transform shear = 0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.089 26.022 Source min/max voxel= 0.089 26.022 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.9235 -0.0265 -0.0611 1.5408 0.0487 0.8839 0.3537 7.1666 0.0493 -0.3642 0.9034 12.1558 Transform center = -2.842 -0.556 -41.550 Transform rotations = -0.383 -0.051 0.051 Transform trans = 4.310 -7.604 16.232 Transform scale = 0.926 0.953 0.975 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Thu Mar 1 02:02:50 UTC 2018 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Mar 1 02:02:52 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4307, pval=0.1049 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Thu Mar 1 02:02:52 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/matt2/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 1 02:02:52 UTC 2018 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.3075 /usr/local/freesurfer/subjects/matt2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3075/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3075/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=4000.00, TE=90.00, TI=-1.00, flip angle=146.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.3075/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 1 02:02:54 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.3075/nu0.mnc ./tmp.mri_nu_correct.mni.3075/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3075/0/ [matt@centos-7-1:/usr/local/freesurfer/subjects/matt2/mri/] [2018-03-01 02:02:54] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3075/0/ ./tmp.mri_nu_correct.mni.3075/nu0.mnc ./tmp.mri_nu_correct.mni.3075/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000953779 -------------------------------------------------------- Iteration 2 Thu Mar 1 02:03:31 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.3075/nu1.mnc ./tmp.mri_nu_correct.mni.3075/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.3075/1/ [matt@centos-7-1:/usr/local/freesurfer/subjects/matt2/mri/] [2018-03-01 02:03:31] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3075/1/ ./tmp.mri_nu_correct.mni.3075/nu1.mnc ./tmp.mri_nu_correct.mni.3075/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 15 CV of field change: 0.00095179 mri_binarize --i ./tmp.mri_nu_correct.mni.3075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3075/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/matt2/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.3075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3075/ones.mgz sysname Linux hostname centos-7-1 machine x86_64 user matt input ./tmp.mri_nu_correct.mni.3075/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.3075/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.3075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3075/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.3075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3075/input.mean.dat sysname Linux hostname centos-7-1 machine x86_64 user matt UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3075/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.3075/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3075/ones.mgz --i ./tmp.mri_nu_correct.mni.3075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3075/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.3075/ones.mgz --i ./tmp.mri_nu_correct.mni.3075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3075/output.mean.dat sysname Linux hostname centos-7-1 machine x86_64 user matt UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3075/ones.mgz Loading ./tmp.mri_nu_correct.mni.3075/nu2.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.3075/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.3075/nu2.mnc ./tmp.mri_nu_correct.mni.3075/nu2.mnc mul 1.08447629773345573907 Saving result to './tmp.mri_nu_correct.mni.3075/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.3075/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.3075/nu2.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.3075/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 3.92902e-10, -1) k_ras = (0, 1, -6.95582e-09) 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 ( 5, 137) to ( 3, 110) Thu Mar 1 02:04:38 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/matt2/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Mar 1 02:04:39 UTC 2018 /usr/local/freesurfer/subjects/matt2/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 0.92355 -0.02645 -0.06107 1.54076; 0.04871 0.88387 0.35371 7.16659; 0.04931 -0.36424 0.90339 12.15576; 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 109 gm peak at 82 (82), valley at 70 (70) csf peak at 42, setting threshold to 68 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 83 (83), valley at 32 (32) csf peak at 42, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 13 seconds. #-------------------------------------------- #@# Skull Stripping Thu Mar 1 02:06:53 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_em_register -rusage /usr/local/freesurfer/subjects/matt2/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 = 1 == 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=8.0 skull bounding box = (50, 19, 12) --> (203, 255, 240) using (101, 98, 126) as brain centroid... mean wm in atlas = 108, using box (82,69,98) --> (119, 127,154) to find MRI wm before smoothing, mri peak at 51 robust fit to distribution - 54 +- 11.3 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.722 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.622153 @ (-9.091, -9.091, -27.273) max log p = -4.604661 @ (31.818, 31.818, 4.545) max log p = -4.593561 @ (-11.364, -25.000, -2.273) max log p = -4.578012 @ (3.409, 7.955, 1.136) max log p = -4.578012 @ (0.000, 0.000, 0.000) max log p = -4.578012 @ (0.000, 0.000, 0.000) Found translation: (14.8, 5.7, -23.9): log p = -4.578 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.433, old_max_log_p =-4.578 (thresh=-4.6) 1.14551 -0.44920 0.11971 39.73551; 0.41775 0.85499 -0.78917 66.06118; 0.20396 0.77170 0.94403 -120.73874; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.359, old_max_log_p =-4.433 (thresh=-4.4) 1.23316 -0.90148 0.04896 76.87475; 0.39556 0.47814 -1.15944 137.27583; 0.77700 1.10196 0.71952 -204.43401; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.298, old_max_log_p =-4.359 (thresh=-4.4) 0.59591 -1.58238 -0.79778 322.58591; -0.13904 0.66357 -1.07313 170.97293; 1.62361 0.47740 0.36805 -202.07112; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.295, old_max_log_p =-4.298 (thresh=-4.3) 0.60048 -1.47484 -0.92356 311.78876; -0.00467 0.98964 -0.97082 108.82121; 1.74996 0.41571 0.54285 -226.70810; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.278, old_max_log_p =-4.295 (thresh=-4.3) 0.58675 -1.53635 -0.80720 316.05164; 0.05145 0.81075 -1.01608 125.63182; 1.78277 0.42350 0.55303 -233.03867; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.275, old_max_log_p =-4.278 (thresh=-4.3) 0.51663 -1.46681 -0.87293 324.53229; -0.04144 0.89615 -0.97754 125.54744; 1.80175 0.39929 0.49280 -226.95627; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.263, old_max_log_p =-4.275 (thresh=-4.3) 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78259 0.42600 0.52028 -230.84703; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.263, old_max_log_p =-4.263 (thresh=-4.3) 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 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 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.263 (old=-4.722) transform before final EM align: 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 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 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 0.56056 -1.44347 -0.87742 315.64517; -0.03585 0.92550 -0.96134 119.07529; 1.78050 0.42550 0.51967 -230.44556; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1213.689238 mri_em_register stimesec 2.281564 mri_em_register ru_maxrss 611656 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157280 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 4 mri_em_register ru_nivcsw 20995 registration took 20 minutes and 19 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/matt2/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=135 y=114 z=108 r=73 first estimation of the main basin volume: 1639971 voxels Looking for seedpoints 2 found in the cerebellum 5 found in the rest of the brain global maximum in x=142, y=105, z=106, Imax=255 CSF=23, 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=3832833952 voxels, voxel volume =1.000 = 3832833952 mmm3 = 3832834.048 cm3 done. PostAnalyze...Basin Prior 113 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin ambiguous basin, non merged: 5 ambiguous voxels; size: 82503 voxels ambiguous basin, non merged: 19 ambiguous voxels; size: 192201 voxels done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=113, z=108, r=8591 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ Problem with the least square interpolation for CSF_MAX Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=52, CSF_intensity=66, CSF_MAX=79 , nb = 2959 RIGHT_CER CSF_MIN=9, CSF_intensity=66, CSF_MAX=70 , nb = -1031394439 LEFT_CER CSF_MIN=11, CSF_intensity=67, CSF_MAX=70 , nb = -1042893155 RIGHT_BRAIN CSF_MIN=50, CSF_intensity=66, CSF_MAX=78 , nb = -1055215142 LEFT_BRAIN CSF_MIN=56, CSF_intensity=67, CSF_MAX=77 , nb = 1075883406 OTHER CSF_MIN=0, CSF_intensity=2, CSF_MAX=6 , nb = 1069601400 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 79, 77, 75, 91 after analyzing : 72, 77, 77, 80 RIGHT_CER before analyzing : 70, 73, 84, 95 after analyzing : 70, 80, 84, 83 LEFT_CER before analyzing : 70, 75, 85, 90 after analyzing : 70, 81, 85, 83 RIGHT_BRAIN before analyzing : 78, 73, 64, 89 after analyzing : 70, 73, 73, 77 LEFT_BRAIN before analyzing : 77, 81, 84, 91 after analyzing : 77, 83, 84, 85 OTHER before analyzing : 6, 19, 75, 91 after analyzing : 6, 56, 75, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...75 iterations *********************VALIDATION********************* curvature mean = -0.017, std = 0.024 curvature mean = 45.567, std = 7.824 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 9.16, sigma = 17.30 after rotation: sse = 9.16, sigma = 17.30 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 12.88, its var is 18.74 before Erosion-Dilatation 15.63% of inacurate vertices after Erosion-Dilatation 29.09% of inacurate vertices 53.00% of 'positive' inacurate vertices 47.00% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...58 iterations mri_strip_skull: done peeling brain Brain Size = 320222 voxels, voxel volume = 1.000 mm3 = 320222 mmm3 = 320.222 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 23.849785 mri_watershed stimesec 0.518234 mri_watershed ru_maxrss 823392 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 206954 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 7992 mri_watershed ru_oublock 600 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 21 mri_watershed ru_nivcsw 656 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Mar 1 02:27:38 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_em_register -rusage /usr/local/freesurfer/subjects/matt2/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 = 1 == 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=25.0 skull bounding box = (95, 86, 58) --> (181, 166, 152) using (124, 113, 105) as brain centroid... mean wm in atlas = 107, using box (114,103,94) --> (134, 122,116) to find MRI wm before smoothing, mri peak at 169 robust fit to distribution - 57 +- 9.1 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.713 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.630957 @ (9.091, 27.273, -9.091) max log p = -4.587218 @ (-22.727, 13.636, -4.545) max log p = -4.570858 @ (2.273, -2.273, -2.273) max log p = -4.570858 @ (0.000, 0.000, 0.000) max log p = -4.570510 @ (-3.977, 0.568, -1.705) max log p = -4.570510 @ (0.000, 0.000, 0.000) Found translation: (-15.3, 39.2, -17.6): log p = -4.571 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.497, old_max_log_p =-4.571 (thresh=-4.6) 0.92586 0.15567 -0.79257 58.64241; -0.56717 0.83758 -0.39627 163.46875; 0.57107 0.72142 0.82208 -156.27986; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.446, old_max_log_p =-4.497 (thresh=-4.5) 1.36882 0.27800 -0.61360 -26.48882; -0.52701 1.08099 -0.57489 130.44052; 0.33187 0.69841 1.06290 -148.63937; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.432, old_max_log_p =-4.446 (thresh=-4.4) 1.51826 0.12442 -0.61466 -28.85547; -0.25894 1.34453 -0.38474 46.68028; 0.42269 0.36522 1.08732 -116.74425; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.416, old_max_log_p =-4.432 (thresh=-4.4) 1.55886 0.08136 -0.80767 -0.41744; -0.27836 1.44537 -0.41360 41.23455; 0.61724 0.37833 0.99779 -135.15230; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.409, old_max_log_p =-4.416 (thresh=-4.4) 1.80448 -0.12826 -0.51628 -43.38441; 0.10261 1.37938 -0.19028 -20.92236; 0.26017 -0.03162 1.33664 -72.01569; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.406, old_max_log_p =-4.409 (thresh=-4.4) 1.82531 -0.08455 -0.34977 -69.03966; 0.02939 1.24002 -0.49001 36.49815; 0.04295 0.36595 1.39601 -92.05534; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.399, old_max_log_p =-4.406 (thresh=-4.4) 1.78878 -0.09336 -0.38834 -57.14050; 0.03136 1.27479 -0.45240 28.40780; 0.10167 0.32224 1.39909 -95.54212; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.390, old_max_log_p =-4.399 (thresh=-4.4) 1.85856 -0.03383 -0.32517 -81.51221; -0.02947 1.27658 -0.44200 36.99011; -0.01955 0.32174 1.39578 -77.23317; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.390, old_max_log_p =-4.390 (thresh=-4.4) 1.85856 -0.03383 -0.32517 -81.51221; -0.02947 1.27658 -0.44200 36.99011; -0.01955 0.32174 1.39578 -77.23317; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.380, old_max_log_p =-4.390 (thresh=-4.4) 1.85181 -0.03099 -0.31264 -81.80318; -0.02934 1.27540 -0.45393 37.92394; -0.03492 0.33205 1.39309 -76.45040; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 10 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.377, old_max_log_p =-4.380 (thresh=-4.4) 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 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 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.377 (old=-4.713) transform before final EM align: 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 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 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 015: -log(p) = 4.6 tol 0.000000 final transform: 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1446.628751 mri_em_register stimesec 3.215219 mri_em_register ru_maxrss 599008 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158572 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 6 mri_em_register ru_nivcsw 39012 registration took 25 minutes and 7 seconds. #-------------------------------------- #@# CA Normalize Thu Mar 1 02:52:44 UTC 2018 /usr/local/freesurfer/subjects/matt2/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=26.0 skull bounding box = (95, 86, 58) --> (181, 166, 152) using (124, 113, 105) as brain centroid... mean wm in atlas = 107, using box (114,103,94) --> (134, 122,116) to find MRI wm before smoothing, mri peak at 169 robust fit to distribution - 57 +- 9.1 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.85181 -0.03099 -0.31264 -81.80318; -0.02937 1.27689 -0.45446 37.82859; -0.03488 0.33166 1.39146 -76.23724; 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 (123, 53, 53) --> (169, 149, 168) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 10 (100.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (96, 52, 55) --> (140, 149, 169) Right_Cerebral_White_Matter: limiting intensities to 155.0 --> 132.0 10 of 10 (100.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 112, 62) --> (155, 145, 101) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 17 (100.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (104, 111, 61) --> (129, 145, 101) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 8 (100.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 111, 81) --> (142, 160, 109) Brain_Stem: limiting intensities to 88.0 --> 132.0 26 of 26 (100.0%) samples deleted using 71 total control points for intensity normalization... 0 of 0 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 53, 53) --> (169, 149, 168) finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (96, 52, 55) --> (140, 149, 169) finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 112, 62) --> (155, 145, 101) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (104, 111, 61) --> (129, 145, 101) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 111, 81) --> (142, 160, 109) skipping region 2 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 53, 53) --> (169, 149, 168) finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (96, 52, 55) --> (140, 149, 169) finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 112, 62) --> (155, 145, 101) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (104, 111, 61) --> (129, 145, 101) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 111, 81) --> (142, 160, 109) skipping region 3 with no control points detected writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 30 seconds. #-------------------------------------- #@# CA Reg Thu Mar 1 02:53:15 UTC 2018 /usr/local/freesurfer/subjects/matt2/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/matt2/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 = 1 == 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) = 3.56 (predicted orig area = 2.2) 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=2.181, neg=0, invalid=762 0001: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0002: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0003: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0004: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0005: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0006: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0007: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0008: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0009: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0010: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0011: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0012: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0013: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0014: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0015: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0016: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0017: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0018: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0019: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0020: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0021: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0022: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0023: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0024: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15565 (16) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26829 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20183 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21683 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30730 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11430 (101) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12076 (102) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14995 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15082 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14161 (67) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15243 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13336 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13252 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18181 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20573 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21969 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.39313 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14181 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11978 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13399 (79) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14159 (79) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10025 (80) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13281 (86) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12801 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.12076 (102) gca peak Left_Cerebral_Cortex = 0.14995 (59) gca peak Left_Lateral_Ventricle = 0.10027 (20) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_White_Matter = 0.18181 (84) gca peak Left_Cerebellum_Cortex = 0.13336 (57) gca peak Left_Thalamus = 0.64095 (94) gca peak Left_Thalamus_Proper = 0.14181 (85) gca peak Left_Caudate = 0.15243 (71) gca peak Left_Putamen = 0.13399 (79) gca peak Left_Pallidum = 0.20183 (93) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak Brain_Stem = 0.10025 (80) gca peak Left_Hippocampus = 0.30730 (58) gca peak Left_Amygdala = 0.21969 (57) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_VentralDC = 0.12801 (89) 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_Cerebral_White_Matter = 0.11430 (101) gca peak Right_Cerebral_Cortex = 0.15082 (58) gca peak Right_Lateral_Ventricle = 0.15565 (16) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_White_Matter = 0.20573 (83) gca peak Right_Cerebellum_Cortex = 0.13252 (56) gca peak Right_Thalamus_Proper = 0.11978 (83) gca peak Right_Caudate = 0.14161 (67) gca peak Right_Putamen = 0.14159 (79) gca peak Right_Pallidum = 0.26829 (96) gca peak Right_Hippocampus = 0.21683 (55) gca peak Right_Amygdala = 0.39313 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_VentralDC = 0.13281 (86) 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 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 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 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=2.181, neg=0, invalid=762 0025: dt=0.005645, rms=2.177 (0.184%), neg=0, invalid=762 0026: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0027: dt=0.850000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0028: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0029: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0030: dt=0.850000, rms=2.177 (-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=2.181, neg=0, invalid=762 0031: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0032: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0033: dt=0.450000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0034: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0035: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0036: dt=0.450000, rms=2.177 (-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=2.181, neg=0, invalid=762 0037: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0038: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0039: dt=0.250000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0040: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0041: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0042: dt=0.250000, rms=2.177 (-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=2.181, neg=0, invalid=762 0043: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0044: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0045: dt=0.150000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0046: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0047: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0048: dt=0.150000, rms=2.177 (-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=2.181, neg=0, invalid=762 0049: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0050: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0051: dt=0.100000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0052: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0053: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0054: dt=0.100000, rms=2.177 (-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=2.181, neg=0, invalid=762 0055: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0056: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0057: dt=0.050000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0058: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0059: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0060: dt=0.050000, rms=2.177 (-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=2.181, neg=0, invalid=762 0061: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0062: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0063: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0064: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0065: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0066: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0067: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0068: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0069: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0070: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0071: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0072: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0073: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0074: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0075: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0076: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0077: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0078: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0079: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0080: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0081: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0082: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0083: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0084: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0085: dt=4734.976000, rms=2.181 (0.000%), neg=0, invalid=762 0086: dt=4734.976000, rms=2.181 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0087: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0088: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0089: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0090: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 0091: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 0092: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0093: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0094: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0095: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0096: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0097: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0098: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0099: dt=46.080000, rms=2.181 (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=2.181, neg=0, invalid=762 0100: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 0101: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 0102: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0103: dt=16.384000, rms=2.181 (0.000%), neg=0, invalid=762 0104: dt=16.384000, rms=2.181 (-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=2.181, neg=0, invalid=762 0105: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0106: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 0 hours, 59 minutes and 55 seconds. mri_ca_register utimesec 3570.074242 mri_ca_register stimesec 2.701018 mri_ca_register ru_maxrss 1282104 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 956195 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 57792 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1 mri_ca_register ru_nivcsw 123043 FSRUNTIME@ mri_ca_register 0.9987 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu Mar 1 03:53:10 UTC 2018 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 centos-7-1 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/matt2/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 = 1 == 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 2.25 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) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17677 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28129 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16930 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24553 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30264 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07580 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07714 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09712 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11620 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30970 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15280 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13902 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14777 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16765 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18739 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29869 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33601 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11131 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11793 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08324 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10360 (77) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08424 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12631 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14500 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.07714 (104) gca peak Left_Cerebral_Cortex = 0.09712 (58) gca peak Left_Lateral_Ventricle = 0.16259 (20) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_White_Matter = 0.16765 (84) gca peak Left_Cerebellum_Cortex = 0.13902 (56) gca peak Left_Thalamus = 1.00000 (94) gca peak Left_Thalamus_Proper = 0.11131 (90) gca peak Left_Caudate = 0.15280 (69) gca peak Left_Putamen = 0.08324 (81) gca peak Left_Pallidum = 0.16930 (96) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_VentralDC = 0.14500 (87) 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_Cerebral_White_Matter = 0.07580 (103) gca peak Right_Cerebral_Cortex = 0.11620 (58) gca peak Right_Lateral_Ventricle = 0.17677 (13) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Cerebellum_White_Matter = 0.18739 (84) gca peak Right_Cerebellum_Cortex = 0.14777 (55) gca peak Right_Thalamus_Proper = 0.11793 (83) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Putamen = 0.10360 (77) gca peak Right_Pallidum = 0.28129 (95) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_VentralDC = 0.12631 (89) 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17677 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28129 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16930 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24553 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30264 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07580 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07714 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09712 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11620 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30970 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15280 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13902 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14777 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16765 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18739 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29869 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33601 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11131 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11793 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08324 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10360 (77) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08424 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12631 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14500 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.07714 (104) gca peak Left_Cerebral_Cortex = 0.09712 (58) gca peak Left_Lateral_Ventricle = 0.16259 (20) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_White_Matter = 0.16765 (84) gca peak Left_Cerebellum_Cortex = 0.13902 (56) gca peak Left_Thalamus = 1.00000 (94) gca peak Left_Thalamus_Proper = 0.11131 (90) gca peak Left_Caudate = 0.15280 (69) gca peak Left_Putamen = 0.08324 (81) gca peak Left_Pallidum = 0.16930 (96) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_VentralDC = 0.14500 (87) 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_Cerebral_White_Matter = 0.07580 (103) gca peak Right_Cerebral_Cortex = 0.11620 (58) gca peak Right_Lateral_Ventricle = 0.17677 (13) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Cerebellum_White_Matter = 0.18739 (84) gca peak Right_Cerebellum_Cortex = 0.14777 (55) gca peak Right_Thalamus_Proper = 0.11793 (83) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Putamen = 0.10360 (77) gca peak Right_Pallidum = 0.28129 (95) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_VentralDC = 0.12631 (89) 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 4819 voxels changed in iteration 0 of unlikely voxel relabeling 1 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 88 gm and wm labels changed (%100 to gray, % 0 to white out of all changed labels) 122 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9086 changed. pass 2: 1297 changed. 3484 voxels changed in iteration 0 of unlikely voxel relabeling 34 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 1924 voxels changed in iteration 0 of unlikely voxel relabeling 3 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 2074 voxels changed in iteration 0 of unlikely voxel relabeling 1 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 2525 voxels changed in iteration 0 of unlikely voxel relabeling 27 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=80 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2483.266443 mri_ca_label stimesec 1.478917 mri_ca_label ru_maxrss 2100748 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 583263 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 208 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 0 mri_ca_label ru_nivcsw 33279 auto-labeling took 41 minutes and 29 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/matt2/mri/transforms/cc_up.lta matt2 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/matt2/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/matt2/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/matt2/mri/norm.mgz 7278 voxels in left wm, 19599 in right wm, xrange [124, 141] searching rotation angles z=[-6 8], y=[-17 -3] searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 global minimum found at slice 136.0, rotations (-10.05, -0.11) final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting