Thu Mar 5 18:06:12 -03 2020 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3 /usr/local/freesurfer/bin/recon-all -s s13_msl3 -autorecon1 -i Sujeto13_MSL_S3_UNI.nii subjid s13_msl3 setenv SUBJECTS_DIR /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream 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 lfa-04 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 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 16384 kbytes maxproc 30755 maxlocks unlimited maxsignal 30755 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8128400 2571068 1200428 131964 4356904 5121636 Swap: 19999740 524 19999216 ######################################## 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: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:12-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/05-21:06:13-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: abraham Machine: lfa-04 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3 mri_convert /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/TEST_DATA/noArtifact/Sujeto13_MSL_S3_UNI.nii /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig/001.mgz mri_convert.bin /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/TEST_DATA/noArtifact/Sujeto13_MSL_S3_UNI.nii /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/TEST_DATA/noArtifact/Sujeto13_MSL_S3_UNI.nii... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999962, -0.00872654, -4.811e-08) j_ras = (0.00872654, 0.999962, -0.0005149) k_ras = (4.5414e-06, 0.00051488, 1) writing to /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Mar 5 18:06:23 -03 2020 Found 1 runs /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig/001.mgz /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/rawavg.mgz /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3 mri_convert /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/rawavg.mgz /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig.mgz --conform mri_convert.bin /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/rawavg.mgz /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/rawavg.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999962, -0.00872654, -4.811e-08) j_ras = (0.00872654, 0.999962, -0.0005149) k_ras = (4.5414e-06, 0.00051488, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig.mgz... mri_add_xform_to_header -c /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/transforms/talairach.xfm /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig.mgz /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 5 18:06:31 -03 2020 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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 lfa-04 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 5 18:06:31 -03 2020 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.32490 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32490/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.32490/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.75632e-10, 0) j_ras = (0, 5.82077e-11, -1) k_ras = (-4.5569e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.32490/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 5 18:06:33 -03 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.32490/nu0.mnc ./tmp.mri_nu_correct.mni.32490/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.32490/0/ -iterations 1000 -distance 50 [abraham@lfa-04:/home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/] [2020-03-05 18:06:33] 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.32490/0/ ./tmp.mri_nu_correct.mni.32490/nu0.mnc ./tmp.mri_nu_correct.mni.32490/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: 0.000998937 mri_convert ./tmp.mri_nu_correct.mni.32490/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.32490/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.32490/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.75632e-10, 0) j_ras = (0, 5.82077e-11, -1) k_ras = (-4.5569e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Mar 5 18:07:23 -03 2020 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 5 18:07:23 -03 2020 Ended at Thu Mar 5 18:07:58 -03 2020 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Mar 5 18:08:00 -03 2020 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5796, pval=0.2817 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/transforms/talairach_avi.log tal_QC_AZS /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/transforms/talairach_avi.log TalAviQA: 0.94944 z-score: -6 #-------------------------------------------- #@# Nu Intensity Correction Thu Mar 5 18:08:00 -03 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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 lfa-04 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 5 18:08:00 -03 2020 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.1338 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1338/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1338/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.75632e-10, 0) j_ras = (0, 5.82077e-11, -1) k_ras = (-4.5569e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1338/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 5 18:08:02 -03 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1338/nu0.mnc ./tmp.mri_nu_correct.mni.1338/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1338/0/ [abraham@lfa-04:/home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/] [2020-03-05 18:08:02] 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.1338/0/ ./tmp.mri_nu_correct.mni.1338/nu0.mnc ./tmp.mri_nu_correct.mni.1338/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 Number of iterations: 15 CV of field change: 0.000938566 -------------------------------------------------------- Iteration 2 Thu Mar 5 18:08:30 -03 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1338/nu1.mnc ./tmp.mri_nu_correct.mni.1338/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1338/1/ [abraham@lfa-04:/home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/] [2020-03-05 18:08:30] 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.1338/1/ ./tmp.mri_nu_correct.mni.1338/nu1.mnc ./tmp.mri_nu_correct.mni.1338/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 4 CV of field change: 0.000992858 mri_binarize --i ./tmp.mri_nu_correct.mni.1338/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1338/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1338/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1338/ones.mgz sysname Linux hostname lfa-04 machine x86_64 user abraham input ./tmp.mri_nu_correct.mni.1338/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1338/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.1338/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1338/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1338/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.1338/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1338/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1338/input.mean.dat sysname Linux hostname lfa-04 machine x86_64 user abraham UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1338/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.1338/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1338/ones.mgz --i ./tmp.mri_nu_correct.mni.1338/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1338/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1338/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.1338/ones.mgz --i ./tmp.mri_nu_correct.mni.1338/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1338/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1338/output.mean.dat sysname Linux hostname lfa-04 machine x86_64 user abraham UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1338/ones.mgz Loading ./tmp.mri_nu_correct.mni.1338/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.1338/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1338/nu2.mnc ./tmp.mri_nu_correct.mni.1338/nu2.mnc mul .99720142181966649323 Saving result to './tmp.mri_nu_correct.mni.1338/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1338/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.1338/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.1338/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.75632e-10, 0) j_ras = (0, 5.82077e-11, -1) k_ras = (-4.5569e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (15, 177) to ( 3, 110) Thu Mar 5 18:09:22 -03 2020 mri_nu_correct.mni done mri_add_xform_to_header -c /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Mar 5 18:09:23 -03 2020 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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 1.33105 -0.05700 -0.08724 2.62387; 0.02523 0.89542 0.27510 -79.81995; 0.03719 -0.06197 1.07634 -80.78894; 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 = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 135 white matter peak found at 115 gm peak at 87 (87), valley at 17 (17) csf peak at 44, setting threshold to 72 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 89 gm peak at 67 (67), valley at 0 (-1) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 25 seconds. #-------------------------------------------- #@# Skull Stripping Thu Mar 5 18:11:49 -03 2020 /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/mri mri_em_register -rusage /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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=39.2 skull bounding box = (40, 0, 0) --> (217, 255, 246) using (99, 85, 123) as brain centroid... mean wm in atlas = 108, using box (77,53,93) --> (120, 116,153) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 9.9 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 = -4.539 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.461351 @ (-9.091, -27.273, 9.091) max log p = -4.330945 @ (4.545, 4.545, -4.545) max log p = -4.311061 @ (2.273, 2.273, -2.273) max log p = -4.277757 @ (-1.136, -1.136, 3.409) max log p = -4.269686 @ (1.705, 0.568, -0.568) max log p = -4.269686 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -21.0, 5.1): log p = -4.270 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.922, old_max_log_p =-4.270 (thresh=-4.3) 1.06375 0.00000 0.00000 -9.77401; 0.00000 1.22567 0.16136 -67.42574; 0.00000 -0.16136 1.22567 7.56914; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.911, old_max_log_p =-3.922 (thresh=-3.9) 1.14353 0.00000 0.00000 -19.87271; 0.00000 1.31760 0.17347 -83.14574; 0.00000 -0.14926 1.13375 15.32069; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.885, old_max_log_p =-3.911 (thresh=-3.9) 1.14353 0.00000 0.00000 -19.87271; 0.00000 1.31760 0.17347 -83.14574; 0.00000 -0.13807 1.04872 22.49088; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.885, old_max_log_p =-3.885 (thresh=-3.9) 1.14353 0.00000 0.00000 -19.87271; 0.00000 1.31760 0.17347 -83.14574; 0.00000 -0.13807 1.04872 22.49088; 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=-3.821, old_max_log_p =-3.885 (thresh=-3.9) 1.12149 -0.00596 0.03461 -21.65523; 0.00265 1.29699 0.13305 -77.87293; -0.04350 -0.09907 1.11316 15.09895; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.821, old_max_log_p =-3.821 (thresh=-3.8) 1.12149 -0.00596 0.03461 -21.65523; 0.00265 1.29699 0.13305 -77.87293; -0.04350 -0.09907 1.11316 15.09895; 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=-3.800, old_max_log_p =-3.821 (thresh=-3.8) 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.800, old_max_log_p =-3.800 (thresh=-3.8) 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.800 (old=-4.539) transform before final EM align: 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.12468 -0.00469 0.01639 -19.41114; 0.00336 1.29540 0.11455 -75.76363; -0.02512 -0.07801 1.11691 9.94463; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1091.696342 mri_em_register stimesec 2.835948 mri_em_register ru_maxrss 614588 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161772 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 0 mri_em_register ru_nivcsw 1799 registration took 18 minutes and 15 seconds. mri_watershed -rusage /home/abraham/Documents/ANALISIS_EXPERIMENTOS/Tests_MP2RAGE/Fujimoto/Primary_stream/s13_msl3/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=127 y=141 z=103 r=107 first estimation of the main basin volume: 5264630 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=149, y=126, z=70, Imax=255 CSF=14, 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=2060824405 voxels, voxel volume =1.000 = 2060824405 mmm3 = 2060824.448 cm3 done. PostAnalyze...Basin Prior 243 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=139, z=98, r=8852 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 28933 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1034875687 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082816573 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1066603324 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1077104570 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1066899762 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 31, 55 after analyzing : 4, 22, 31, 30 RIGHT_CER before analyzing : 4, 5, 33, 64 after analyzing : 4, 23, 33, 33 LEFT_CER before analyzing : 4, 6, 35, 57 after analyzing : 4, 25, 35, 33 RIGHT_BRAIN before analyzing : 5, 7, 30, 54 after analyzing : 5, 22, 30, 30 LEFT_BRAIN before analyzing : 5, 7, 31, 55 after analyzing : 5, 23, 31, 31 OTHER before analyzing : 4, 7, 61, 92 after analyzing : 4, 43, 61, 55 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 67.971, std = 7.395 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.30, sigma = 3.71 after rotation: sse = 2.30, sigma = 3.71 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.32, its var is 3.06 before Erosion-Dilatation 0.14% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1302814 voxels, voxel volume = 1.000 mm3 = 1302814 mmm3 = 1302.814 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 21.430538 mri_watershed stimesec 0.219984 mri_watershed ru_maxrss 870132 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215901 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2176 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 20 mri_watershed done cp brainmask.auto.mgz brainmask.mgz Started at Thu Mar 5 18:06:12 -03 2020 Ended at Thu Mar 5 18:30:26 -03 2020 #@#%# recon-all-run-time-hours 0.404 recon-all -s s13_msl3 finished without error at Thu Mar 5 18:30:26 -03 2020 New invocation of recon-all Mon Mar 9 12:56:15 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3 /usr/local/freesurfer/bin/recon-all -s s13_msl3/ -autorecon2 -autorecon3 subjid s13_msl3 setenv SUBJECTS_DIR /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask 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 lfa03-workstation 4.15.0-60-generic #67~16.04.1-Ubuntu SMP Mon Aug 26 08:57:33 UTC 2019 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 unlimited maxproc 95849 maxlocks unlimited maxsignal 95849 maxmessage 819200 maxnice 0 maxrtprio 50 maxrttime unlimited total used free shared buff/cache available Mem: 24598588 2717180 18353572 513896 3527836 20907400 Swap: 8000508 0 8000508 ######################################## 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: 2020/03/09-15:56:15-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:15-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:15-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:16-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:17-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/09-15:56:18-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: lfa-03 Machine: lfa03-workstation Platform: Linux PlatformVersion: 4.15.0-60-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Mon Mar 9 12:56:18 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri mri_em_register -rusage /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/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=21.1 skull bounding box = (63, 84, 24) --> (194, 196, 190) using (107, 121, 107) as brain centroid... mean wm in atlas = 107, using box (91,107,87) --> (123, 134,127) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 4.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.420 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.014141 @ (-9.091, -27.273, 9.091) max log p = -3.787520 @ (4.545, 4.545, -4.545) max log p = -3.783315 @ (2.273, -2.273, 2.273) max log p = -3.751617 @ (-1.136, -1.136, 1.136) max log p = -3.750571 @ (0.568, 3.977, -0.568) max log p = -3.749646 @ (1.420, -0.852, 0.284) Found translation: (-1.4, -23.0, 7.7): log p = -3.750 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.328, old_max_log_p =-3.750 (thresh=-3.7) 1.07500 0.00000 0.00000 -11.03229; 0.00000 1.14016 0.15011 -57.63292; 0.00000 -0.13885 1.05465 22.08532; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.328, old_max_log_p =-3.328 (thresh=-3.3) 1.07500 0.00000 0.00000 -11.03229; 0.00000 1.14016 0.15011 -57.63292; 0.00000 -0.13885 1.05465 22.08532; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.246, old_max_log_p =-3.328 (thresh=-3.3) 1.09323 -0.04106 0.02902 -10.36308; 0.03647 1.13940 0.15115 -60.42665; -0.03718 -0.14137 1.07385 25.33222; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.246, old_max_log_p =-3.246 (thresh=-3.2) 1.09323 -0.04106 0.02902 -10.36308; 0.03647 1.13940 0.15115 -60.42665; -0.03718 -0.14137 1.07385 25.33222; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.224, old_max_log_p =-3.246 (thresh=-3.2) 1.09443 -0.03300 0.03915 -13.56257; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.223, old_max_log_p =-3.224 (thresh=-3.2) 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 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 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.223 (old=-4.420) transform before final EM align: 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 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 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 430.903209 mri_em_register stimesec 0.983943 mri_em_register ru_maxrss 603100 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162497 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 141544 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 15 mri_em_register ru_nivcsw 8858 registration took 7 minutes and 12 seconds. #-------------------------------------- #@# CA Normalize Mon Mar 9 13:03:31 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/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=22.0 skull bounding box = (63, 84, 24) --> (194, 196, 192) using (107, 121, 108) as brain centroid... mean wm in atlas = 107, using box (91,107,87) --> (123, 134,128) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 4.6 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 1.09571 -0.03303 0.03920 -13.72698; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 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 (128, 81, 26) --> (189, 182, 180) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 344 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 84, 24) --> (129, 185, 179) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 370 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 160, 50) --> (176, 197, 100) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 28 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 160, 47) --> (131, 197, 100) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 150, 83) --> (146, 212, 111) Brain_Stem: limiting intensities to 88.0 --> 132.0 7 of 27 (25.9%) samples deleted using 778 total control points for intensity normalization... bias field = 0.966 +- 0.047 0 of 771 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 81, 26) --> (189, 182, 180) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 416 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 84, 24) --> (129, 185, 179) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 456 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 160, 50) --> (176, 197, 100) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 112 (16.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 160, 47) --> (131, 197, 100) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 75 (22.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 150, 83) --> (146, 212, 111) Brain_Stem: limiting intensities to 88.0 --> 132.0 57 of 91 (62.6%) samples deleted using 1150 total control points for intensity normalization... bias field = 0.997 +- 0.047 0 of 1046 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 81, 26) --> (189, 182, 180) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 605 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 84, 24) --> (129, 185, 179) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 536 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 160, 50) --> (176, 197, 100) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 40 of 86 (46.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 160, 47) --> (131, 197, 100) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 64 (50.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 150, 83) --> (146, 212, 111) Brain_Stem: limiting intensities to 88.0 --> 132.0 128 of 180 (71.1%) samples deleted using 1471 total control points for intensity normalization... bias field = 1.009 +- 0.045 3 of 1249 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 55 seconds. #-------------------------------------- #@# CA Reg Mon Mar 9 13:04:26 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri mri_ca_register -rusage /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/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) = 1.37 (predicted orig area = 5.8) 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=0.871, neg=0, invalid=762 0001: dt=219.821109, rms=0.822 (5.579%), neg=0, invalid=762 0002: dt=140.301299, rms=0.809 (1.666%), neg=0, invalid=762 0003: dt=517.888000, rms=0.792 (1.995%), neg=0, invalid=762 0004: dt=110.976000, rms=0.785 (0.894%), neg=0, invalid=762 0005: dt=517.888000, rms=0.778 (0.956%), neg=0, invalid=762 0006: dt=129.472000, rms=0.776 (0.294%), neg=0, invalid=762 0007: dt=887.808000, rms=0.769 (0.802%), neg=0, invalid=762 0008: dt=92.480000, rms=0.767 (0.315%), neg=0, invalid=762 0009: dt=517.888000, rms=0.765 (0.234%), neg=0, invalid=762 0010: dt=517.888000, rms=0.765 (-0.223%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.766, neg=0, invalid=762 0011: dt=110.976000, rms=0.764 (0.206%), neg=0, invalid=762 0012: dt=92.480000, rms=0.764 (0.011%), neg=0, invalid=762 0013: dt=92.480000, rms=0.764 (0.002%), neg=0, invalid=762 0014: dt=92.480000, rms=0.764 (0.011%), neg=0, invalid=762 0015: dt=92.480000, rms=0.764 (0.009%), neg=0, invalid=762 0016: dt=92.480000, rms=0.764 (-0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.767, neg=0, invalid=762 0017: dt=211.243243, rms=0.740 (3.451%), neg=0, invalid=762 0018: dt=110.349084, rms=0.728 (1.617%), neg=0, invalid=762 0019: dt=116.635514, rms=0.722 (0.778%), neg=0, invalid=762 0020: dt=103.680000, rms=0.717 (0.808%), neg=0, invalid=762 0021: dt=79.687636, rms=0.713 (0.452%), neg=0, invalid=762 0022: dt=180.433735, rms=0.708 (0.699%), neg=0, invalid=762 0023: dt=66.857143, rms=0.705 (0.439%), neg=0, invalid=762 0024: dt=165.859155, rms=0.702 (0.515%), neg=0, invalid=762 0025: dt=65.600000, rms=0.699 (0.310%), neg=0, invalid=762 0026: dt=145.152000, rms=0.697 (0.422%), neg=0, invalid=762 0027: dt=36.288000, rms=0.695 (0.181%), neg=0, invalid=762 0028: dt=36.288000, rms=0.695 (0.087%), neg=0, invalid=762 0029: dt=36.288000, rms=0.694 (0.143%), neg=0, invalid=762 0030: dt=36.288000, rms=0.692 (0.221%), neg=0, invalid=762 0031: dt=36.288000, rms=0.690 (0.293%), neg=0, invalid=762 0032: dt=36.288000, rms=0.688 (0.335%), neg=0, invalid=762 0033: dt=36.288000, rms=0.685 (0.353%), neg=0, invalid=762 0034: dt=36.288000, rms=0.683 (0.357%), neg=0, invalid=762 0035: dt=36.288000, rms=0.681 (0.355%), neg=0, invalid=762 0036: dt=36.288000, rms=0.678 (0.327%), neg=0, invalid=762 0037: dt=36.288000, rms=0.676 (0.302%), neg=0, invalid=762 0038: dt=36.288000, rms=0.674 (0.279%), neg=0, invalid=762 0039: dt=36.288000, rms=0.673 (0.240%), neg=0, invalid=762 0040: dt=36.288000, rms=0.671 (0.201%), neg=0, invalid=762 0041: dt=36.288000, rms=0.670 (0.168%), neg=0, invalid=762 0042: dt=36.288000, rms=0.669 (0.147%), neg=0, invalid=762 0043: dt=36.288000, rms=0.668 (0.126%), neg=0, invalid=762 0044: dt=36.288000, rms=0.668 (0.117%), neg=0, invalid=762 0045: dt=36.288000, rms=0.667 (0.112%), neg=0, invalid=762 0046: dt=145.152000, rms=0.667 (0.025%), neg=0, invalid=762 0047: dt=145.152000, rms=0.667 (0.015%), neg=0, invalid=762 0048: dt=145.152000, rms=0.667 (0.003%), neg=0, invalid=762 0049: dt=145.152000, rms=0.666 (0.052%), neg=0, invalid=762 0050: dt=145.152000, rms=0.666 (0.052%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0051: dt=22.000000, rms=0.666 (0.147%), neg=0, invalid=762 0052: dt=0.001270, rms=0.666 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.686, neg=0, invalid=762 0053: dt=0.000000, rms=0.686 (0.104%), neg=0, invalid=762 0054: dt=0.000000, rms=0.686 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.686, neg=0, invalid=762 0055: dt=0.000000, rms=0.686 (0.104%), neg=0, invalid=762 0056: dt=0.000000, rms=0.686 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.748, neg=0, invalid=762 0057: dt=4.827795, rms=0.732 (2.065%), neg=0, invalid=762 0058: dt=2.536585, rms=0.731 (0.134%), neg=0, invalid=762 0059: dt=2.536585, rms=0.731 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0060: dt=0.000000, rms=0.731 (0.092%), neg=0, invalid=762 0061: dt=0.000000, rms=0.731 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.795, neg=0, invalid=762 0062: dt=1.280000, rms=0.791 (0.533%), neg=0, invalid=762 0063: dt=2.240000, rms=0.785 (0.759%), neg=0, invalid=762 0064: dt=0.320000, rms=0.785 (0.019%), neg=0, invalid=762 0065: dt=0.320000, rms=0.785 (0.020%), neg=0, invalid=762 0066: dt=0.320000, rms=0.785 (0.017%), neg=0, invalid=762 0067: dt=0.320000, rms=0.785 (0.003%), neg=0, invalid=762 0068: dt=1.792000, rms=0.783 (0.170%), neg=0, invalid=762 0069: dt=0.000000, rms=0.783 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.784, neg=0, invalid=762 0070: dt=1.024000, rms=0.783 (0.167%), neg=0, invalid=762 0071: dt=1.792000, rms=0.782 (0.119%), neg=0, invalid=762 0072: dt=1.792000, rms=0.782 (-0.119%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.748, neg=0, invalid=762 0073: dt=1.065895, rms=0.716 (4.301%), neg=0, invalid=762 0074: dt=0.096000, rms=0.714 (0.199%), neg=0, invalid=762 0075: dt=0.096000, rms=0.714 (-0.121%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.715, neg=0, invalid=762 0076: dt=0.028000, rms=0.714 (0.114%), neg=0, invalid=762 0077: dt=0.007000, rms=0.714 (0.001%), neg=0, invalid=762 0078: dt=0.007000, rms=0.714 (0.001%), neg=0, invalid=762 0079: dt=0.007000, rms=0.714 (-0.004%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.09091 (15) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (97 voxels, overlap=0.264) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (97 voxels, peak = 14), gca=13.7 gca peak = 0.15565 (16) mri peak = 0.07529 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (153 voxels, overlap=0.211) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (153 voxels, peak = 10), gca=10.3 gca peak = 0.26829 (96) mri peak = 0.08347 (94) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (632 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (632 voxels, peak = 93), gca=92.6 gca peak = 0.20183 (93) mri peak = 0.07229 (90) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (509 voxels, overlap=1.013) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (509 voxels, peak = 89), gca=88.8 gca peak = 0.21683 (55) mri peak = 0.12705 (51) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (456 voxels, overlap=0.955) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (456 voxels, peak = 50), gca=50.3 gca peak = 0.30730 (58) mri peak = 0.13782 (52) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (481 voxels, overlap=0.827) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (481 voxels, peak = 52), gca=51.9 gca peak = 0.11430 (101) mri peak = 0.10178 (105) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (47107 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (47107 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.09572 (106) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46302 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46302 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.04221 (55) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (10892 voxels, overlap=0.970) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (10892 voxels, peak = 56), gca=55.8 gca peak = 0.15082 (58) mri peak = 0.04096 (53) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (12697 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (12697 voxels, peak = 52), gca=51.9 gca peak = 0.14161 (67) mri peak = 0.07583 (65) Right_Caudate (50): linear fit = 0.98 x + 0.0 (633 voxels, overlap=0.970) Right_Caudate (50): linear fit = 0.98 x + 0.0 (633 voxels, peak = 65), gca=65.3 gca peak = 0.15243 (71) mri peak = 0.07639 (74) Left_Caudate (11): linear fit = 0.94 x + 0.0 (715 voxels, overlap=0.968) Left_Caudate (11): linear fit = 0.94 x + 0.0 (715 voxels, peak = 66), gca=66.4 gca peak = 0.13336 (57) mri peak = 0.05074 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (8518 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (8518 voxels, peak = 55), gca=55.0 gca peak = 0.13252 (56) mri peak = 0.04812 (55) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (9174 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (9174 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.08922 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5362 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5362 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.09661 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4619 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4619 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.10435 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (279 voxels, overlap=0.986) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (279 voxels, peak = 51), gca=51.0 gca peak = 0.39313 (56) mri peak = 0.13169 (53) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (378 voxels, overlap=0.878) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (378 voxels, peak = 52), gca=51.8 gca peak = 0.14181 (85) mri peak = 0.05013 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4339 voxels, overlap=0.962) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4339 voxels, peak = 85), gca=84.6 gca peak = 0.11978 (83) mri peak = 0.06603 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3518 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3518 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.05520 (76) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1747 voxels, overlap=0.996) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1747 voxels, peak = 80), gca=80.2 gca peak = 0.14159 (79) mri peak = 0.05240 (78) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1888 voxels, overlap=1.000) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1888 voxels, peak = 77), gca=77.0 gca peak = 0.10025 (80) mri peak = 0.09618 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8283 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8283 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07203 (88) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (952 voxels, overlap=0.710) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (952 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.06848 (96) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1063 voxels, overlap=0.852) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1063 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.10118 ( 4) gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.66 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=762 0080: dt=129.472000, rms=0.727 (0.850%), neg=0, invalid=762 0081: dt=129.472000, rms=0.726 (0.185%), neg=0, invalid=762 0082: dt=129.472000, rms=0.725 (0.144%), neg=0, invalid=762 0083: dt=110.976000, rms=0.725 (0.065%), neg=0, invalid=762 0084: dt=221.952000, rms=0.724 (0.108%), neg=0, invalid=762 0085: dt=92.480000, rms=0.723 (0.049%), neg=0, invalid=762 0086: dt=92.480000, rms=0.723 (0.057%), neg=0, invalid=762 0087: dt=92.480000, rms=0.722 (0.077%), neg=0, invalid=762 0088: dt=92.480000, rms=0.722 (0.077%), neg=0, invalid=762 0089: dt=92.480000, rms=0.721 (0.074%), neg=0, invalid=762 0090: dt=92.480000, rms=0.721 (0.075%), neg=0, invalid=762 0091: dt=92.480000, rms=0.720 (0.087%), neg=0, invalid=762 0092: dt=92.480000, rms=0.720 (0.081%), neg=0, invalid=762 0093: dt=92.480000, rms=0.719 (0.073%), neg=0, invalid=762 0094: dt=92.480000, rms=0.719 (0.067%), neg=0, invalid=762 0095: dt=92.480000, rms=0.718 (0.076%), neg=0, invalid=762 0096: dt=92.480000, rms=0.718 (0.068%), neg=0, invalid=762 0097: dt=92.480000, rms=0.717 (0.059%), neg=0, invalid=762 0098: dt=92.480000, rms=0.717 (0.062%), neg=0, invalid=762 0099: dt=92.480000, rms=0.716 (0.059%), neg=0, invalid=762 0100: dt=92.480000, rms=0.716 (0.051%), neg=0, invalid=762 0101: dt=92.480000, rms=0.716 (0.047%), neg=0, invalid=762 0102: dt=92.480000, rms=0.715 (0.046%), neg=0, invalid=762 0103: dt=92.480000, rms=0.715 (0.044%), neg=0, invalid=762 0104: dt=92.480000, rms=0.715 (0.052%), neg=0, invalid=762 0105: dt=92.480000, rms=0.714 (0.053%), neg=0, invalid=762 0106: dt=92.480000, rms=0.714 (0.056%), neg=0, invalid=762 0107: dt=92.480000, rms=0.713 (0.058%), neg=0, invalid=762 0108: dt=92.480000, rms=0.713 (0.063%), neg=0, invalid=762 0109: dt=92.480000, rms=0.712 (0.065%), neg=0, invalid=762 0110: dt=92.480000, rms=0.712 (0.068%), neg=0, invalid=762 0111: dt=92.480000, rms=0.711 (0.065%), neg=0, invalid=762 0112: dt=92.480000, rms=0.711 (0.065%), neg=0, invalid=762 0113: dt=92.480000, rms=0.711 (0.064%), neg=0, invalid=762 0114: dt=92.480000, rms=0.710 (0.063%), neg=0, invalid=762 0115: dt=92.480000, rms=0.710 (0.059%), neg=0, invalid=762 0116: dt=92.480000, rms=0.709 (0.057%), neg=0, invalid=762 0117: dt=92.480000, rms=0.709 (0.051%), neg=0, invalid=762 0118: dt=92.480000, rms=0.709 (0.047%), neg=0, invalid=762 0119: dt=92.480000, rms=0.708 (0.047%), neg=0, invalid=762 0120: dt=92.480000, rms=0.708 (0.045%), neg=0, invalid=762 0121: dt=92.480000, rms=0.708 (0.039%), neg=0, invalid=762 0122: dt=92.480000, rms=0.707 (0.034%), neg=0, invalid=762 0123: dt=92.480000, rms=0.707 (0.031%), neg=0, invalid=762 0124: dt=92.480000, rms=0.707 (0.030%), neg=0, invalid=762 0125: dt=92.480000, rms=0.707 (0.029%), neg=0, invalid=762 0126: dt=92.480000, rms=0.707 (0.027%), neg=0, invalid=762 0127: dt=92.480000, rms=0.706 (0.026%), neg=0, invalid=762 0128: dt=92.480000, rms=0.706 (0.026%), neg=0, invalid=762 0129: dt=92.480000, rms=0.706 (0.025%), neg=0, invalid=762 0130: dt=92.480000, rms=0.706 (0.028%), neg=0, invalid=762 0131: dt=92.480000, rms=0.706 (0.027%), neg=0, invalid=762 0132: dt=92.480000, rms=0.706 (0.024%), neg=0, invalid=762 0133: dt=92.480000, rms=0.705 (0.021%), neg=0, invalid=762 0134: dt=443.904000, rms=0.705 (0.004%), neg=0, invalid=762 0135: dt=443.904000, rms=0.705 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.706, neg=0, invalid=762 0136: dt=55.488000, rms=0.705 (0.173%), neg=0, invalid=762 0137: dt=27.744000, rms=0.705 (0.005%), neg=0, invalid=762 0138: dt=27.744000, rms=0.705 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=762 0139: dt=248.832000, rms=0.695 (1.563%), neg=0, invalid=762 0140: dt=90.074074, rms=0.688 (1.019%), neg=0, invalid=762 0141: dt=80.447837, rms=0.685 (0.392%), neg=0, invalid=762 0142: dt=133.019608, rms=0.682 (0.534%), neg=0, invalid=762 0143: dt=36.288000, rms=0.680 (0.307%), neg=0, invalid=762 0144: dt=331.776000, rms=0.675 (0.677%), neg=0, invalid=762 0145: dt=75.921569, rms=0.672 (0.504%), neg=0, invalid=762 0146: dt=36.288000, rms=0.670 (0.191%), neg=0, invalid=762 0147: dt=414.720000, rms=0.667 (0.465%), neg=0, invalid=762 0148: dt=70.530612, rms=0.664 (0.434%), neg=0, invalid=762 0149: dt=36.288000, rms=0.663 (0.134%), neg=0, invalid=762 0150: dt=497.664000, rms=0.661 (0.370%), neg=0, invalid=762 0151: dt=59.076923, rms=0.659 (0.362%), neg=0, invalid=762 0152: dt=62.208000, rms=0.658 (0.084%), neg=0, invalid=762 0153: dt=145.152000, rms=0.657 (0.116%), neg=0, invalid=762 0154: dt=36.288000, rms=0.657 (0.074%), neg=0, invalid=762 0155: dt=580.608000, rms=0.654 (0.363%), neg=0, invalid=762 0156: dt=36.288000, rms=0.653 (0.173%), neg=0, invalid=762 0157: dt=145.152000, rms=0.653 (0.082%), neg=0, invalid=762 0158: dt=62.208000, rms=0.652 (0.055%), neg=0, invalid=762 0159: dt=145.152000, rms=0.652 (0.068%), neg=0, invalid=762 0160: dt=36.288000, rms=0.652 (0.042%), neg=0, invalid=762 0161: dt=36.288000, rms=0.652 (0.022%), neg=0, invalid=762 0162: dt=36.288000, rms=0.651 (0.038%), neg=0, invalid=762 0163: dt=36.288000, rms=0.651 (0.052%), neg=0, invalid=762 0164: dt=36.288000, rms=0.651 (0.062%), neg=0, invalid=762 0165: dt=36.288000, rms=0.650 (0.074%), neg=0, invalid=762 0166: dt=36.288000, rms=0.650 (0.081%), neg=0, invalid=762 0167: dt=36.288000, rms=0.649 (0.089%), neg=0, invalid=762 0168: dt=36.288000, rms=0.648 (0.088%), neg=0, invalid=762 0169: dt=36.288000, rms=0.648 (0.084%), neg=0, invalid=762 0170: dt=36.288000, rms=0.648 (0.006%), neg=0, invalid=762 0171: dt=36.288000, rms=0.648 (0.018%), neg=0, invalid=762 0172: dt=36.288000, rms=0.648 (0.030%), neg=0, invalid=762 0173: dt=36.288000, rms=0.647 (0.011%), neg=0, invalid=762 0174: dt=36.288000, rms=0.647 (0.023%), neg=0, invalid=762 0175: dt=1.134000, rms=0.647 (0.000%), neg=0, invalid=762 0176: dt=0.567000, rms=0.647 (0.000%), neg=0, invalid=762 0177: dt=0.141750, rms=0.647 (0.000%), neg=0, invalid=762 0178: dt=0.017719, rms=0.647 (0.000%), neg=0, invalid=762 0179: dt=0.008859, rms=0.647 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0180: dt=68.923077, rms=0.646 (0.389%), neg=0, invalid=762 0181: dt=36.288000, rms=0.645 (0.052%), neg=0, invalid=762 0182: dt=62.208000, rms=0.645 (0.046%), neg=0, invalid=762 0183: dt=62.208000, rms=0.645 (0.070%), neg=0, invalid=762 0184: dt=62.208000, rms=0.644 (0.080%), neg=0, invalid=762 0185: dt=62.208000, rms=0.644 (0.039%), neg=0, invalid=762 0186: dt=62.208000, rms=0.644 (0.039%), neg=0, invalid=762 0187: dt=62.208000, rms=0.643 (0.102%), neg=0, invalid=762 0188: dt=62.208000, rms=0.642 (0.151%), neg=0, invalid=762 0189: dt=62.208000, rms=0.641 (0.158%), neg=0, invalid=762 0190: dt=62.208000, rms=0.640 (0.139%), neg=0, invalid=762 0191: dt=62.208000, rms=0.639 (0.122%), neg=0, invalid=762 0192: dt=62.208000, rms=0.639 (0.120%), neg=0, invalid=762 0193: dt=62.208000, rms=0.637 (0.167%), neg=0, invalid=762 0194: dt=62.208000, rms=0.636 (0.181%), neg=0, invalid=762 0195: dt=62.208000, rms=0.635 (0.160%), neg=0, invalid=762 0196: dt=62.208000, rms=0.634 (0.146%), neg=0, invalid=762 0197: dt=62.208000, rms=0.634 (0.141%), neg=0, invalid=762 0198: dt=62.208000, rms=0.633 (0.062%), neg=0, invalid=762 0199: dt=62.208000, rms=0.633 (0.036%), neg=0, invalid=762 0200: dt=62.208000, rms=0.633 (0.055%), neg=0, invalid=762 0201: dt=15.552000, rms=0.632 (0.006%), neg=0, invalid=762 0202: dt=15.552000, rms=0.632 (0.005%), neg=0, invalid=762 0203: dt=1.620000, rms=0.632 (0.001%), neg=0, invalid=762 0204: dt=0.006328, rms=0.632 (0.000%), neg=0, invalid=762 0205: dt=0.003164, rms=0.632 (0.000%), neg=0, invalid=762 0206: dt=0.000012, rms=0.632 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=762 0207: dt=0.000000, rms=0.637 (0.151%), neg=0, invalid=762 0208: dt=0.000000, rms=0.637 (0.000%), neg=0, invalid=762 0209: dt=0.000000, rms=0.637 (0.000%), neg=0, invalid=762 0210: dt=0.000000, rms=0.637 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=762 0211: dt=122.841994, rms=0.624 (2.160%), neg=0, invalid=762 0212: dt=11.200000, rms=0.621 (0.508%), neg=0, invalid=762 0213: dt=11.200000, rms=0.619 (0.348%), neg=0, invalid=762 0214: dt=11.200000, rms=0.617 (0.270%), neg=0, invalid=762 0215: dt=0.700000, rms=0.617 (0.015%), neg=0, invalid=762 0216: dt=0.350000, rms=0.617 (0.008%), neg=0, invalid=762 0217: dt=0.175000, rms=0.617 (0.004%), neg=0, invalid=762 0218: dt=0.010937, rms=0.617 (0.001%), neg=0, invalid=762 0219: dt=0.002344, rms=0.617 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.629, neg=0, invalid=762 0220: dt=0.000000, rms=0.628 (0.136%), neg=0, invalid=762 0221: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=762 0222: dt=0.000018, rms=0.628 (0.000%), neg=0, invalid=762 0223: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=762 0224: dt=0.000000, rms=0.628 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.629, neg=0, invalid=762 0225: dt=0.000000, rms=0.628 (0.136%), neg=0, invalid=762 0226: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=762 0227: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=762 0228: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0229: dt=1.792000, rms=0.643 (1.465%), neg=0, invalid=762 0230: dt=4.096000, rms=0.639 (0.671%), neg=0, invalid=762 0231: dt=0.000000, rms=0.639 (-0.007%), neg=0, invalid=762 0232: dt=0.100000, rms=0.639 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=762 0233: dt=1.792000, rms=0.638 (0.282%), neg=0, invalid=762 0234: dt=4.096000, rms=0.637 (0.238%), neg=0, invalid=762 0235: dt=7.168000, rms=0.635 (0.219%), neg=0, invalid=762 0236: dt=0.000000, rms=0.635 (-0.001%), neg=0, invalid=762 0237: dt=0.100000, rms=0.635 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.620, neg=0, invalid=762 0238: dt=0.448000, rms=0.594 (4.077%), neg=0, invalid=762 0239: dt=0.448000, rms=0.587 (1.208%), neg=0, invalid=762 0240: dt=0.448000, rms=0.583 (0.650%), neg=0, invalid=762 0241: dt=0.448000, rms=0.581 (0.401%), neg=0, invalid=762 0242: dt=0.448000, rms=0.579 (0.303%), neg=0, invalid=762 0243: dt=0.448000, rms=0.578 (0.228%), neg=0, invalid=762 0244: dt=0.448000, rms=0.577 (0.188%), neg=0, invalid=762 0245: dt=0.571429, rms=0.576 (0.190%), neg=0, invalid=762 0246: dt=0.448000, rms=0.575 (0.123%), neg=0, invalid=762 0247: dt=0.448000, rms=0.574 (0.101%), neg=0, invalid=762 0248: dt=0.448000, rms=0.574 (0.087%), neg=0, invalid=762 0249: dt=0.448000, rms=0.574 (0.074%), neg=0, invalid=762 0250: dt=0.448000, rms=0.573 (0.069%), neg=0, invalid=762 0251: dt=0.448000, rms=0.573 (0.056%), neg=0, invalid=762 0252: dt=0.448000, rms=0.573 (0.054%), neg=0, invalid=762 0253: dt=0.448000, rms=0.572 (0.042%), neg=0, invalid=762 0254: dt=0.448000, rms=0.572 (0.042%), neg=0, invalid=762 0255: dt=0.448000, rms=0.572 (0.068%), neg=0, invalid=762 0256: dt=0.448000, rms=0.572 (0.024%), neg=0, invalid=762 0257: dt=0.448000, rms=0.571 (0.049%), neg=0, invalid=762 0258: dt=0.448000, rms=0.571 (0.063%), neg=0, invalid=762 0259: dt=0.448000, rms=0.571 (0.066%), neg=0, invalid=762 0260: dt=0.448000, rms=0.570 (0.059%), neg=0, invalid=762 0261: dt=0.448000, rms=0.570 (0.054%), neg=0, invalid=762 0262: dt=0.448000, rms=0.570 (0.038%), neg=0, invalid=762 0263: dt=0.448000, rms=0.570 (0.017%), neg=0, invalid=762 0264: dt=0.448000, rms=0.570 (0.004%), neg=0, invalid=762 0265: dt=0.000010, rms=0.570 (0.000%), neg=0, invalid=762 0266: dt=0.000010, rms=0.570 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=762 0267: dt=0.448000, rms=0.560 (1.899%), neg=0, invalid=762 0268: dt=0.448000, rms=0.558 (0.365%), neg=0, invalid=762 0269: dt=0.500000, rms=0.557 (0.195%), neg=0, invalid=762 0270: dt=0.448000, rms=0.556 (0.040%), neg=0, invalid=762 0271: dt=0.448000, rms=0.556 (0.020%), neg=0, invalid=762 0272: dt=0.448000, rms=0.556 (0.002%), neg=0, invalid=762 0273: dt=0.448000, rms=0.556 (-0.066%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 0274: dt=27.744000, rms=0.553 (0.185%), neg=0, invalid=762 0275: dt=0.018063, rms=0.553 (0.001%), neg=0, invalid=762 0276: dt=0.018063, rms=0.553 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 0277: dt=0.000000, rms=0.553 (0.171%), neg=0, invalid=762 0278: dt=0.000000, rms=0.553 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 0279: dt=31.104000, rms=0.552 (0.306%), neg=0, invalid=762 0280: dt=25.920000, rms=0.552 (0.041%), neg=0, invalid=762 0281: dt=25.920000, rms=0.552 (0.012%), neg=0, invalid=762 0282: dt=25.920000, rms=0.552 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0283: dt=16.829630, rms=0.551 (0.370%), neg=0, invalid=762 0284: dt=9.072000, rms=0.551 (0.027%), neg=0, invalid=762 0285: dt=9.072000, rms=0.550 (0.014%), neg=0, invalid=762 0286: dt=9.072000, rms=0.550 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0287: dt=25.396825, rms=0.543 (1.489%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0288: dt=38.400000, rms=0.540 (0.541%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0289: dt=11.200000, rms=0.540 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0290: dt=11.200000, rms=0.540 (0.018%), neg=0, invalid=762 0291: dt=11.200000, rms=0.540 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0292: dt=11.200000, rms=0.540 (-0.072%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0293: dt=18.127168, rms=0.534 (1.252%), neg=0, invalid=762 0294: dt=38.400000, rms=0.529 (0.927%), neg=0, invalid=762 0295: dt=37.639344, rms=0.527 (0.472%), neg=0, invalid=762 0296: dt=11.200000, rms=0.525 (0.239%), neg=0, invalid=762 0297: dt=11.200000, rms=0.525 (0.099%), neg=0, invalid=762 0298: dt=11.200000, rms=0.524 (0.144%), neg=0, invalid=762 0299: dt=11.200000, rms=0.523 (0.178%), neg=0, invalid=762 0300: dt=11.200000, rms=0.522 (0.219%), neg=0, invalid=762 0301: dt=11.200000, rms=0.521 (0.239%), neg=0, invalid=762 0302: dt=11.200000, rms=0.520 (0.249%), neg=0, invalid=762 0303: dt=11.200000, rms=0.518 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0304: dt=11.200000, rms=0.517 (0.228%), neg=0, invalid=762 0305: dt=11.200000, rms=0.516 (0.213%), neg=0, invalid=762 0306: dt=11.200000, rms=0.515 (0.184%), neg=0, invalid=762 0307: dt=11.200000, rms=0.514 (0.176%), neg=0, invalid=762 0308: dt=11.200000, rms=0.513 (0.178%), neg=0, invalid=762 0309: dt=11.200000, rms=0.512 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0310: dt=11.200000, rms=0.511 (0.174%), neg=0, invalid=762 0311: dt=11.200000, rms=0.511 (0.155%), neg=0, invalid=762 0312: dt=11.200000, rms=0.510 (0.120%), neg=0, invalid=762 0313: dt=11.200000, rms=0.509 (0.105%), neg=0, invalid=762 0314: dt=44.800000, rms=0.509 (0.040%), neg=0, invalid=762 0315: dt=44.800000, rms=0.509 (-0.066%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0316: dt=4.547368, rms=0.513 (0.536%), neg=0, invalid=762 0317: dt=0.576000, rms=0.513 (-0.001%), neg=0, invalid=762 0318: dt=0.576000, rms=0.513 (0.002%), neg=0, invalid=762 0319: dt=0.576000, rms=0.513 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0320: dt=0.250000, rms=0.513 (0.176%), neg=0, invalid=762 0321: dt=0.063000, rms=0.513 (0.000%), neg=0, invalid=762 0322: dt=0.063000, rms=0.513 (0.001%), neg=0, invalid=762 0323: dt=0.063000, rms=0.513 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0324: dt=0.112000, rms=0.523 (0.172%), neg=0, invalid=762 0325: dt=0.004000, rms=0.523 (0.000%), neg=0, invalid=762 0326: dt=0.004000, rms=0.523 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0327: dt=1.024000, rms=0.522 (0.353%), neg=0, invalid=762 0328: dt=0.384000, rms=0.522 (0.012%), neg=0, invalid=762 0329: dt=0.384000, rms=0.522 (-0.005%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 iter 0, gcam->neg = 986 after 11 iterations, nbhd size=1, neg = 0 0330: dt=2.035748, rms=0.469 (8.050%), neg=0, invalid=762 0331: dt=0.028000, rms=0.469 (0.022%), neg=0, invalid=762 0332: dt=0.028000, rms=0.469 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0333: dt=0.112000, rms=0.468 (0.389%), neg=0, invalid=762 0334: dt=0.024000, rms=0.468 (0.005%), neg=0, invalid=762 0335: dt=0.024000, rms=0.468 (-0.002%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0336: dt=0.000000, rms=0.455 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0337: dt=32.368000, rms=0.454 (0.114%), neg=0, invalid=762 0338: dt=4.624000, rms=0.454 (0.000%), neg=0, invalid=762 0339: dt=4.624000, rms=0.454 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0340: dt=0.567000, rms=0.454 (0.000%), neg=0, invalid=762 0341: dt=0.121500, rms=0.454 (0.000%), neg=0, invalid=762 0342: dt=0.121500, rms=0.454 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0343: dt=9.072000, rms=0.454 (0.013%), neg=0, invalid=762 0344: dt=2.268000, rms=0.454 (0.001%), neg=0, invalid=762 0345: dt=2.268000, rms=0.454 (0.000%), neg=0, invalid=762 0346: dt=2.268000, rms=0.454 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0347: dt=2.800000, rms=0.455 (0.045%), neg=0, invalid=762 0348: dt=0.700000, rms=0.455 (0.002%), neg=0, invalid=762 0349: dt=0.700000, rms=0.455 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0350: dt=11.200000, rms=0.454 (0.159%), neg=0, invalid=762 0351: dt=38.400000, rms=0.453 (0.243%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0352: dt=75.636364, rms=0.451 (0.402%), neg=0, invalid=762 0353: dt=9.600000, rms=0.450 (0.106%), neg=0, invalid=762 0354: dt=9.600000, rms=0.450 (0.006%), neg=0, invalid=762 0355: dt=9.600000, rms=0.450 (-0.028%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0356: dt=2.558140, rms=0.452 (0.108%), neg=0, invalid=762 0357: dt=0.000000, rms=0.452 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0358: dt=10.443730, rms=0.450 (0.435%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0359: dt=23.798319, rms=0.446 (0.906%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0360: dt=3.619048, rms=0.446 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0361: dt=3.619048, rms=0.446 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0362: dt=0.000050, rms=0.451 (0.000%), neg=0, invalid=762 0363: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0364: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.442, neg=0, invalid=762 iter 0, gcam->neg = 700 after 13 iterations, nbhd size=1, neg = 0 0365: dt=1.479873, rms=0.429 (2.911%), neg=0, invalid=762 0366: dt=0.000013, rms=0.429 (0.000%), neg=0, invalid=762 0367: dt=0.000013, rms=0.429 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0368: dt=0.112000, rms=0.429 (0.115%), neg=0, invalid=762 0369: dt=0.064000, rms=0.428 (0.023%), neg=0, invalid=762 0370: dt=0.064000, rms=0.428 (0.008%), neg=0, invalid=762 0371: dt=0.064000, rms=0.428 (-0.038%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 17 minutes and 9 seconds. mri_ca_register utimesec 4626.029648 mri_ca_register stimesec 2.627969 mri_ca_register ru_maxrss 1330728 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 3349168 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 63160 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 9 mri_ca_register ru_nivcsw 7726 FSRUNTIME@ mri_ca_register 1.2858 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Mar 9 14:21:35 -03 2020 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 lfa03-workstation machine x86_64 setenv SUBJECTS_DIR /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask cd /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/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 5.84 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.17012 ( 2) Left_Lateral_Ventricle (4): linear fit = 0.05 x + 0.0 (198 voxels, overlap=0.014) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (198 voxels, peak = 1), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.15152 ( 2) Right_Lateral_Ventricle (43): linear fit = 0.03 x + 0.0 (191 voxels, overlap=0.424) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (191 voxels, peak = 0), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.08755 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, peak = 95), gca=94.5 gca peak = 0.16930 (96) mri peak = 0.09016 (97) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (483 voxels, overlap=1.016) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (483 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.15209 (51) Right_Hippocampus: unreasonable value (49.8/51.0), not in range [50, 90] - rejecting gca peak = 0.30264 (59) mri peak = 0.13001 (52) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (446 voxels, overlap=0.892) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (446 voxels, peak = 53), gca=52.8 gca peak = 0.07580 (103) mri peak = 0.10630 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27484 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27484 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.10211 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26799 voxels, overlap=0.566) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26799 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.04416 (54) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (15577 voxels, overlap=0.881) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (15577 voxels, peak = 55), gca=54.8 gca peak = 0.11620 (58) mri peak = 0.04562 (55) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (16796 voxels, overlap=0.918) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (16796 voxels, peak = 53), gca=53.1 gca peak = 0.30970 (66) mri peak = 0.07831 (64) Right_Caudate (50): linear fit = 0.95 x + 0.0 (821 voxels, overlap=1.013) Right_Caudate (50): linear fit = 0.95 x + 0.0 (821 voxels, peak = 63), gca=63.0 gca peak = 0.15280 (69) mri peak = 0.08221 (67) Left_Caudate (11): linear fit = 0.93 x + 0.0 (701 voxels, overlap=1.008) Left_Caudate (11): linear fit = 0.93 x + 0.0 (701 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.05612 (56) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10850 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10850 voxels, peak = 55), gca=55.2 gca peak = 0.14777 (55) mri peak = 0.05415 (56) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (10986 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (10986 voxels, peak = 57), gca=57.5 gca peak = 0.16765 (84) mri peak = 0.10662 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (4040 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (4040 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.10399 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (3760 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (3760 voxels, peak = 88), gca=87.8 gca peak = 0.29869 (57) mri peak = 0.08651 (51) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (346 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (346 voxels, peak = 54), gca=53.9 gca peak = 0.33601 (57) mri peak = 0.11810 (55) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (338 voxels, overlap=1.018) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (338 voxels, peak = 51), gca=51.0 gca peak = 0.11131 (90) mri peak = 0.06724 (84) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3182 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3182 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.07038 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3174 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3174 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.06434 (76) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1455 voxels, overlap=0.984) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1455 voxels, peak = 79), gca=79.0 gca peak = 0.10360 (77) mri peak = 0.05588 (69) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1577 voxels, overlap=0.888) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1577 voxels, peak = 74), gca=74.3 gca peak = 0.08424 (78) mri peak = 0.09127 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8142 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8142 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.06854 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (964 voxels, overlap=0.799) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (964 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.07725 (96) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1003 voxels, overlap=0.724) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1003 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 1.00000 ( 9) gca peak = 0.19357 (14) mri peak = 0.24906 ( 2) Fourth_Ventricle (15): linear fit = 0.03 x + 0.0 (69 voxels, overlap=0.014) Fourth_Ventricle (15): linear fit = 0.03 x + 0.0 (69 voxels, peak = 0), gca=0.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 0.89 x + 0: 53 estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30837 ( 7) mri peak = 0.17012 ( 2) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (198 voxels, overlap=0.754) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (198 voxels, peak = 1), gca=2.8 gca peak = 0.30173 ( 5) mri peak = 0.15152 ( 2) Right_Lateral_Ventricle (43): linear fit = 0.17 x + 0.0 (191 voxels, overlap=0.893) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (191 voxels, peak = 1), gca=2.0 gca peak = 0.28139 (93) mri peak = 0.08755 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, peak = 93), gca=92.5 gca peak = 0.16717 (99) mri peak = 0.09016 (97) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (483 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (483 voxels, peak = 100), gca=100.5 gca peak = 0.32293 (50) mri peak = 0.15209 (51) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (540 voxels, overlap=0.985) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (540 voxels, peak = 50), gca=50.0 gca peak = 0.29578 (53) mri peak = 0.13001 (52) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (446 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (446 voxels, peak = 52), gca=51.7 gca peak = 0.07614 (105) mri peak = 0.10630 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27484 voxels, overlap=0.686) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27484 voxels, peak = 104), gca=104.5 gca peak = 0.07686 (107) mri peak = 0.10211 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26799 voxels, overlap=0.677) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26799 voxels, peak = 107), gca=107.0 gca peak = 0.10324 (55) mri peak = 0.04416 (54) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (15577 voxels, overlap=0.994) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (15577 voxels, peak = 54), gca=54.2 gca peak = 0.12629 (53) mri peak = 0.04562 (55) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16796 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16796 voxels, peak = 52), gca=52.2 gca peak = 0.34192 (63) mri peak = 0.07831 (64) Right_Caudate (50): linear fit = 1.00 x + 0.0 (821 voxels, overlap=1.011) Right_Caudate (50): linear fit = 1.00 x + 0.0 (821 voxels, peak = 63), gca=63.0 gca peak = 0.13199 (64) mri peak = 0.08221 (67) Left_Caudate (11): linear fit = 1.03 x + 0.0 (701 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.03 x + 0.0 (701 voxels, peak = 66), gca=66.2 gca peak = 0.14509 (55) mri peak = 0.05612 (56) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10850 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10850 voxels, peak = 55), gca=55.0 gca peak = 0.14202 (57) mri peak = 0.05415 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10986 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10986 voxels, peak = 55), gca=55.0 gca peak = 0.15881 (87) mri peak = 0.10662 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4040 voxels, overlap=0.929) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4040 voxels, peak = 87), gca=86.6 gca peak = 0.17046 (88) mri peak = 0.10399 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3760 voxels, overlap=0.921) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3760 voxels, peak = 89), gca=89.3 gca peak = 0.29805 (54) mri peak = 0.08651 (51) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (346 voxels, overlap=1.028) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (346 voxels, peak = 53), gca=52.7 gca peak = 0.36313 (51) mri peak = 0.11810 (55) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (338 voxels, overlap=1.006) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (338 voxels, peak = 51), gca=51.0 gca peak = 0.11253 (86) mri peak = 0.06724 (84) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3182 voxels, overlap=0.996) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3182 voxels, peak = 86), gca=85.6 gca peak = 0.11611 (85) mri peak = 0.07038 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3174 voxels, overlap=0.995) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3174 voxels, peak = 85), gca=84.6 gca peak = 0.08313 (79) mri peak = 0.06434 (76) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1455 voxels, overlap=0.983) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1455 voxels, peak = 80), gca=80.2 gca peak = 0.09182 (72) mri peak = 0.05588 (69) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1577 voxels, overlap=0.993) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1577 voxels, peak = 73), gca=73.1 gca peak = 0.07750 (86) mri peak = 0.09127 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8142 voxels, overlap=0.766) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8142 voxels, peak = 86), gca=86.0 gca peak = 0.11472 (96) mri peak = 0.06854 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (964 voxels, overlap=0.893) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (964 voxels, peak = 96), gca=96.0 gca peak = 0.16451 (92) mri peak = 0.07725 (96) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1003 voxels, overlap=0.930) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1003 voxels, peak = 94), gca=94.3 gca peak = 0.33708 (10) mri peak = 1.00000 ( 9) gca peak = 0.45928 ( 6) mri peak = 0.24906 ( 2) Fourth_Ventricle (15): linear fit = 0.16 x + 0.0 (69 voxels, overlap=0.051) Fourth_Ventricle (15): linear fit = 0.16 x + 0.0 (69 voxels, peak = 1), gca=0.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.19080 (30) gca peak Left_Thalamus = 0.64095 (86) gca peak Third_Ventricle = 0.33708 (10) gca peak Fourth_Ventricle = 0.45928 ( 6) gca peak CSF = 0.26605 (13) gca peak Left_Accumbens_area = 0.54630 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.26981 (21) gca peak Right_Accumbens_area = 0.34583 (62) gca peak Right_vessel = 0.83220 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65560 (13) gca peak WM_hypointensities = 0.07141 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.70615 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 89058 voxels changed in iteration 0 of unlikely voxel relabeling 305 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35484 gm and wm labels changed (%17 to gray, %83 to white out of all changed labels) 317 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 79923 changed. image ll: -2.174, PF=0.500 pass 2: 24834 changed. image ll: -2.174, PF=0.500 pass 3: 7591 changed. pass 4: 2655 changed. 60133 voxels changed in iteration 0 of unlikely voxel relabeling 269 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 6764 voxels changed in iteration 0 of unlikely voxel relabeling 48 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5983 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4774 voxels changed in iteration 0 of unlikely voxel relabeling 22 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1948.737193 mri_ca_label stimesec 1.103966 mri_ca_label ru_maxrss 2104112 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1120656 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 480 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 9 mri_ca_label ru_nivcsw 15485 auto-labeling took 32 minutes and 30 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri/transforms/cc_up.lta s13_msl3 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri/transforms/cc_up.lta reading aseg from /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri/aseg.auto_noCCseg.mgz reading norm from /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri/norm.mgz 23371 voxels in left wm, 11966 in right wm, xrange [126, 131] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -6.6 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 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 global minimum found at slice 127.4, rotations (0.41, 0.35) final transformation (x=127.4, yr=0.407, zr=0.352): 0.99996 -0.00614 0.00710 0.75421; 0.00614 0.99998 0.00004 1.21605; -0.00710 -0.00000 0.99997 36.90607; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 126 92 eigenvectors: -0.00019 -0.00002 1.00000; 0.04606 -0.99894 -0.00001; 0.99894 0.04606 0.00019; error in mid anterior detected - correcting... writing aseg with callosum to /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri/aseg.auto.mgz... corpus callosum segmentation took 0.3 minutes #-------------------------------------- #@# Merge ASeg Mon Mar 9 14:54:23 -03 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Mar 9 14:54:23 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 753 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 59 (59), valley at 0 (-1) csf peak at 29, setting threshold to 49 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 60 (60), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 51 seconds. #-------------------------------------------- #@# Mask BFS Mon Mar 9 14:56:16 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1350185 voxels in mask (pct= 8.05) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Mar 9 14:56:17 -03 2020 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 107.2 +- 5.3 [79.0 --> 125.0] GM (65.0) : 63.7 +- 11.2 [30.0 --> 95.0] setting bottom of white matter range to 74.9 setting top of gray matter range to 86.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 13659 sparsely connected voxels removed... thickening thin strands.... 20 segments, 14007 filled 3716 bright non-wm voxels segmented. 10425 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.29 minutes reading wm segmentation from wm.seg.mgz... 209 voxels added to wm to prevent paths from MTL structures to cortex 2068 additional wm voxels added 0 additional wm voxels added SEG EDIT: 44751 voxels turned on, 52601 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 117 new 117 115,126,128 old 117 new 117 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 97 found - 97 modified | TOTAL: 97 pass 2 (xy+): 0 found - 97 modified | TOTAL: 97 pass 1 (xy-): 93 found - 93 modified | TOTAL: 190 pass 2 (xy-): 0 found - 93 modified | TOTAL: 190 pass 1 (yz+): 152 found - 152 modified | TOTAL: 342 pass 2 (yz+): 0 found - 152 modified | TOTAL: 342 pass 1 (yz-): 118 found - 118 modified | TOTAL: 460 pass 2 (yz-): 0 found - 118 modified | TOTAL: 460 pass 1 (xz+): 100 found - 100 modified | TOTAL: 560 pass 2 (xz+): 0 found - 100 modified | TOTAL: 560 pass 1 (xz-): 102 found - 102 modified | TOTAL: 662 pass 2 (xz-): 0 found - 102 modified | TOTAL: 662 Iteration Number : 1 pass 1 (+++): 206 found - 206 modified | TOTAL: 206 pass 2 (+++): 0 found - 206 modified | TOTAL: 206 pass 1 (+++): 155 found - 155 modified | TOTAL: 361 pass 2 (+++): 0 found - 155 modified | TOTAL: 361 pass 1 (+++): 284 found - 284 modified | TOTAL: 645 pass 2 (+++): 0 found - 284 modified | TOTAL: 645 pass 1 (+++): 183 found - 183 modified | TOTAL: 828 pass 2 (+++): 0 found - 183 modified | TOTAL: 828 Iteration Number : 1 pass 1 (++): 326 found - 326 modified | TOTAL: 326 pass 2 (++): 0 found - 326 modified | TOTAL: 326 pass 1 (+-): 281 found - 281 modified | TOTAL: 607 pass 2 (+-): 0 found - 281 modified | TOTAL: 607 pass 1 (--): 264 found - 264 modified | TOTAL: 871 pass 2 (--): 1 found - 265 modified | TOTAL: 872 pass 3 (--): 0 found - 265 modified | TOTAL: 872 pass 1 (-+): 290 found - 290 modified | TOTAL: 1162 pass 2 (-+): 0 found - 290 modified | TOTAL: 1162 Iteration Number : 2 pass 1 (xy+): 46 found - 46 modified | TOTAL: 46 pass 2 (xy+): 0 found - 46 modified | TOTAL: 46 pass 1 (xy-): 50 found - 50 modified | TOTAL: 96 pass 2 (xy-): 0 found - 50 modified | TOTAL: 96 pass 1 (yz+): 58 found - 58 modified | TOTAL: 154 pass 2 (yz+): 0 found - 58 modified | TOTAL: 154 pass 1 (yz-): 61 found - 61 modified | TOTAL: 215 pass 2 (yz-): 0 found - 61 modified | TOTAL: 215 pass 1 (xz+): 62 found - 62 modified | TOTAL: 277 pass 2 (xz+): 0 found - 62 modified | TOTAL: 277 pass 1 (xz-): 67 found - 67 modified | TOTAL: 344 pass 2 (xz-): 0 found - 67 modified | TOTAL: 344 Iteration Number : 2 pass 1 (+++): 9 found - 9 modified | TOTAL: 9 pass 2 (+++): 0 found - 9 modified | TOTAL: 9 pass 1 (+++): 11 found - 11 modified | TOTAL: 20 pass 2 (+++): 0 found - 11 modified | TOTAL: 20 pass 1 (+++): 12 found - 12 modified | TOTAL: 32 pass 2 (+++): 0 found - 12 modified | TOTAL: 32 pass 1 (+++): 17 found - 17 modified | TOTAL: 49 pass 2 (+++): 0 found - 17 modified | TOTAL: 49 Iteration Number : 2 pass 1 (++): 39 found - 39 modified | TOTAL: 39 pass 2 (++): 0 found - 39 modified | TOTAL: 39 pass 1 (+-): 39 found - 39 modified | TOTAL: 78 pass 2 (+-): 0 found - 39 modified | TOTAL: 78 pass 1 (--): 29 found - 29 modified | TOTAL: 107 pass 2 (--): 0 found - 29 modified | TOTAL: 107 pass 1 (-+): 35 found - 35 modified | TOTAL: 142 pass 2 (-+): 0 found - 35 modified | TOTAL: 142 Iteration Number : 3 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 8 found - 8 modified | TOTAL: 13 pass 2 (xy-): 0 found - 8 modified | TOTAL: 13 pass 1 (yz+): 11 found - 11 modified | TOTAL: 24 pass 2 (yz+): 0 found - 11 modified | TOTAL: 24 pass 1 (yz-): 7 found - 7 modified | TOTAL: 31 pass 2 (yz-): 0 found - 7 modified | TOTAL: 31 pass 1 (xz+): 3 found - 3 modified | TOTAL: 34 pass 2 (xz+): 0 found - 3 modified | TOTAL: 34 pass 1 (xz-): 4 found - 4 modified | TOTAL: 38 pass 2 (xz-): 0 found - 4 modified | TOTAL: 38 Iteration Number : 3 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 3 found - 3 modified | TOTAL: 9 pass 2 (+++): 0 found - 3 modified | TOTAL: 9 pass 1 (+++): 2 found - 2 modified | TOTAL: 11 pass 2 (+++): 0 found - 2 modified | TOTAL: 11 Iteration Number : 3 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 4 found - 4 modified | TOTAL: 8 pass 2 (+-): 0 found - 4 modified | TOTAL: 8 pass 1 (--): 4 found - 4 modified | TOTAL: 12 pass 2 (--): 0 found - 4 modified | TOTAL: 12 pass 1 (-+): 7 found - 7 modified | TOTAL: 19 pass 2 (-+): 0 found - 7 modified | TOTAL: 19 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3262 (out of 535777: 0.608835) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Mar 9 14:57:37 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.09571 -0.03303 0.03920 -13.72699; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.09571 -0.03303 0.03920 -13.72699; 0.02728 1.13985 0.15979 -59.67096; -0.04647 -0.15055 1.07356 28.31185; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1330 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 111, 92), TAL = (2.0, -36.0, 17.0) talairach voxel to voxel transform 0.91057 0.02157 -0.03646 14.81894; -0.02679 0.85976 -0.12699 54.53023; 0.03566 0.12150 0.91210 -18.08357; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 111, 92) --> (2.0, -36.0, 17.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (2.00, -36.00, 17.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -36.00, 17.00) SRC: (112.20, 135.39, 83.17) search lh wm seed point around talairach space (-16.00, -36.00, 17.00), SRC: (144.98, 134.42, 84.45) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Mon Mar 9 14:58:00 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 14 found - 14 modified | TOTAL: 27 pass 2 (xy-): 0 found - 14 modified | TOTAL: 27 pass 1 (yz+): 18 found - 18 modified | TOTAL: 45 pass 2 (yz+): 0 found - 18 modified | TOTAL: 45 pass 1 (yz-): 12 found - 12 modified | TOTAL: 57 pass 2 (yz-): 0 found - 12 modified | TOTAL: 57 pass 1 (xz+): 8 found - 8 modified | TOTAL: 65 pass 2 (xz+): 0 found - 8 modified | TOTAL: 65 pass 1 (xz-): 9 found - 9 modified | TOTAL: 74 pass 2 (xz-): 0 found - 9 modified | TOTAL: 74 Iteration Number : 1 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 7 found - 7 modified | TOTAL: 10 pass 2 (+++): 0 found - 7 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 4 found - 4 modified | TOTAL: 8 pass 2 (+-): 0 found - 4 modified | TOTAL: 8 pass 1 (--): 2 found - 2 modified | TOTAL: 10 pass 2 (--): 0 found - 2 modified | TOTAL: 10 pass 1 (-+): 7 found - 7 modified | TOTAL: 17 pass 2 (-+): 0 found - 7 modified | TOTAL: 17 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 105 (out of 262085: 0.040063) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 4044 vertices, 4431 faces slice 40: 16097 vertices, 16739 faces slice 50: 29870 vertices, 30610 faces slice 60: 44270 vertices, 45028 faces slice 70: 58742 vertices, 59568 faces slice 80: 72013 vertices, 72873 faces slice 90: 86817 vertices, 87715 faces slice 100: 101892 vertices, 102900 faces slice 110: 116797 vertices, 117893 faces slice 120: 130599 vertices, 131733 faces slice 130: 142365 vertices, 143431 faces slice 140: 153180 vertices, 154323 faces slice 150: 164189 vertices, 165345 faces slice 160: 173416 vertices, 174558 faces slice 170: 180834 vertices, 181960 faces slice 180: 186738 vertices, 187808 faces slice 190: 188952 vertices, 189896 faces slice 200: 188952 vertices, 189896 faces slice 210: 188952 vertices, 189896 faces slice 220: 188952 vertices, 189896 faces slice 230: 188952 vertices, 189896 faces slice 240: 188952 vertices, 189896 faces slice 250: 188952 vertices, 189896 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 188952 voxel in cpt #1: X=-944 [v=188952,e=569688,f=379792] located at (-30.100723, -31.916561, -10.930956) For the whole surface: X=-944 [v=188952,e=569688,f=379792] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Mar 9 14:58:04 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 4 found - 4 modified | TOTAL: 8 pass 2 (xy-): 0 found - 4 modified | TOTAL: 8 pass 1 (yz+): 8 found - 8 modified | TOTAL: 16 pass 2 (yz+): 0 found - 8 modified | TOTAL: 16 pass 1 (yz-): 7 found - 7 modified | TOTAL: 23 pass 2 (yz-): 0 found - 7 modified | TOTAL: 23 pass 1 (xz+): 2 found - 2 modified | TOTAL: 25 pass 2 (xz+): 0 found - 2 modified | TOTAL: 25 pass 1 (xz-): 6 found - 6 modified | TOTAL: 31 pass 2 (xz-): 0 found - 6 modified | TOTAL: 31 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 5 found - 5 modified | TOTAL: 6 pass 2 (-+): 0 found - 5 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 42 (out of 254032: 0.016533) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 2337 vertices, 2560 faces slice 40: 11265 vertices, 11767 faces slice 50: 22280 vertices, 22868 faces slice 60: 34324 vertices, 35016 faces slice 70: 47838 vertices, 48616 faces slice 80: 61321 vertices, 62059 faces slice 90: 76246 vertices, 77149 faces slice 100: 91215 vertices, 92193 faces slice 110: 105999 vertices, 107043 faces slice 120: 120050 vertices, 121105 faces slice 130: 132332 vertices, 133369 faces slice 140: 143400 vertices, 144475 faces slice 150: 153961 vertices, 155012 faces slice 160: 163156 vertices, 164185 faces slice 170: 170967 vertices, 171966 faces slice 180: 176995 vertices, 177949 faces slice 190: 180351 vertices, 181215 faces slice 200: 180384 vertices, 181232 faces slice 210: 180384 vertices, 181232 faces slice 220: 180384 vertices, 181232 faces slice 230: 180384 vertices, 181232 faces slice 240: 180384 vertices, 181232 faces slice 250: 180384 vertices, 181232 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 180384 voxel in cpt #1: X=-848 [v=180384,e=543696,f=362464] located at (30.406771, -27.919693, -11.374324) For the whole surface: X=-848 [v=180384,e=543696,f=362464] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Mar 9 14:58:08 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Mon Mar 9 14:58:13 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Mar 9 14:58:18 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.6 mm, total surface area = 95621 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.188 (target=0.015) step 005: RMS=0.145 (target=0.015) step 010: RMS=0.116 (target=0.015) step 015: RMS=0.105 (target=0.015) step 020: RMS=0.100 (target=0.015) step 025: RMS=0.097 (target=0.015) step 030: RMS=0.096 (target=0.015) step 035: RMS=0.095 (target=0.015) step 040: RMS=0.094 (target=0.015) step 045: RMS=0.093 (target=0.015) step 050: RMS=0.094 (target=0.015) step 055: RMS=0.094 (target=0.015) step 060: RMS=0.095 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.673414 mris_inflate stimesec 0.083994 mris_inflate ru_maxrss 248080 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 60511 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 13336 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 99 #-------------------------------------------- #@# Inflation1 rh Mon Mar 9 14:58:57 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.2 mm, total surface area = 91038 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.188 (target=0.015) step 005: RMS=0.145 (target=0.015) step 010: RMS=0.117 (target=0.015) step 015: RMS=0.103 (target=0.015) step 020: RMS=0.098 (target=0.015) step 025: RMS=0.096 (target=0.015) step 030: RMS=0.093 (target=0.015) step 035: RMS=0.092 (target=0.015) step 040: RMS=0.091 (target=0.015) step 045: RMS=0.091 (target=0.015) step 050: RMS=0.091 (target=0.015) step 055: RMS=0.091 (target=0.015) step 060: RMS=0.091 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.349010 mris_inflate stimesec 0.035997 mris_inflate ru_maxrss 236924 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 57722 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12728 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 171 #-------------------------------------------- #@# QSphere lh Mon Mar 9 14:59:35 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.92 +- 0.68 (0.00-->9.28) (max @ vno 133923 --> 135119) face area 0.02 +- 0.04 (-0.40-->1.32) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.618, avgs=0 005/300: dt: 0.9000, rms radial error=176.363, avgs=0 010/300: dt: 0.9000, rms radial error=175.817, avgs=0 015/300: dt: 0.9000, rms radial error=175.101, avgs=0 020/300: dt: 0.9000, rms radial error=174.290, avgs=0 025/300: dt: 0.9000, rms radial error=173.424, avgs=0 030/300: dt: 0.9000, rms radial error=172.527, avgs=0 035/300: dt: 0.9000, rms radial error=171.614, avgs=0 040/300: dt: 0.9000, rms radial error=170.695, avgs=0 045/300: dt: 0.9000, rms radial error=169.774, avgs=0 050/300: dt: 0.9000, rms radial error=168.854, avgs=0 055/300: dt: 0.9000, rms radial error=167.937, avgs=0 060/300: dt: 0.9000, rms radial error=167.024, avgs=0 065/300: dt: 0.9000, rms radial error=166.115, avgs=0 070/300: dt: 0.9000, rms radial error=165.210, avgs=0 075/300: dt: 0.9000, rms radial error=164.310, avgs=0 080/300: dt: 0.9000, rms radial error=163.415, avgs=0 085/300: dt: 0.9000, rms radial error=162.524, avgs=0 090/300: dt: 0.9000, rms radial error=161.638, avgs=0 095/300: dt: 0.9000, rms radial error=160.756, avgs=0 100/300: dt: 0.9000, rms radial error=159.879, avgs=0 105/300: dt: 0.9000, rms radial error=159.007, avgs=0 110/300: dt: 0.9000, rms radial error=158.140, avgs=0 115/300: dt: 0.9000, rms radial error=157.277, avgs=0 120/300: dt: 0.9000, rms radial error=156.419, avgs=0 125/300: dt: 0.9000, rms radial error=155.566, avgs=0 130/300: dt: 0.9000, rms radial error=154.717, avgs=0 135/300: dt: 0.9000, rms radial error=153.872, avgs=0 140/300: dt: 0.9000, rms radial error=153.032, avgs=0 145/300: dt: 0.9000, rms radial error=152.197, avgs=0 150/300: dt: 0.9000, rms radial error=151.365, avgs=0 155/300: dt: 0.9000, rms radial error=150.538, avgs=0 160/300: dt: 0.9000, rms radial error=149.716, avgs=0 165/300: dt: 0.9000, rms radial error=148.898, avgs=0 170/300: dt: 0.9000, rms radial error=148.084, avgs=0 175/300: dt: 0.9000, rms radial error=147.275, avgs=0 180/300: dt: 0.9000, rms radial error=146.470, avgs=0 185/300: dt: 0.9000, rms radial error=145.669, avgs=0 190/300: dt: 0.9000, rms radial error=144.873, avgs=0 195/300: dt: 0.9000, rms radial error=144.082, avgs=0 200/300: dt: 0.9000, rms radial error=143.297, avgs=0 205/300: dt: 0.9000, rms radial error=142.516, avgs=0 210/300: dt: 0.9000, rms radial error=141.740, avgs=0 215/300: dt: 0.9000, rms radial error=140.967, avgs=0 220/300: dt: 0.9000, rms radial error=140.199, avgs=0 225/300: dt: 0.9000, rms radial error=139.435, avgs=0 230/300: dt: 0.9000, rms radial error=138.675, avgs=0 235/300: dt: 0.9000, rms radial error=137.919, avgs=0 240/300: dt: 0.9000, rms radial error=137.167, avgs=0 245/300: dt: 0.9000, rms radial error=136.418, avgs=0 250/300: dt: 0.9000, rms radial error=135.674, avgs=0 255/300: dt: 0.9000, rms radial error=134.933, avgs=0 260/300: dt: 0.9000, rms radial error=134.197, avgs=0 265/300: dt: 0.9000, rms radial error=133.464, avgs=0 270/300: dt: 0.9000, rms radial error=132.735, avgs=0 275/300: dt: 0.9000, rms radial error=132.011, avgs=0 280/300: dt: 0.9000, rms radial error=131.285, avgs=0 285/300: dt: 0.9000, rms radial error=130.563, avgs=0 290/300: dt: 0.9000, rms radial error=129.845, avgs=0 295/300: dt: 0.9000, rms radial error=129.130, avgs=0 300/300: dt: 0.9000, rms radial error=128.420, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23238.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00064 epoch 2 (K=40.0), pass 1, starting sse = 4617.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00161 epoch 3 (K=160.0), pass 1, starting sse = 940.00 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/10 = 0.00733 epoch 4 (K=640.0), pass 1, starting sse = 389.12 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/15 = 0.01047 final distance error %38.53 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 214.233994 mris_sphere stimesec 0.108001 mris_sphere ru_maxrss 248724 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 60526 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 13336 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 2503 FSRUNTIME@ mris_sphere 0.0596 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Mar 9 15:03:10 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.92 +- 0.63 (0.00-->8.74) (max @ vno 100898 --> 102309) face area 0.02 +- 0.03 (-0.29-->0.69) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.508, avgs=0 005/300: dt: 0.9000, rms radial error=177.251, avgs=0 010/300: dt: 0.9000, rms radial error=176.700, avgs=0 015/300: dt: 0.9000, rms radial error=175.976, avgs=0 020/300: dt: 0.9000, rms radial error=175.152, avgs=0 025/300: dt: 0.9000, rms radial error=174.271, avgs=0 030/300: dt: 0.9000, rms radial error=173.358, avgs=0 035/300: dt: 0.9000, rms radial error=172.428, avgs=0 040/300: dt: 0.9000, rms radial error=171.492, avgs=0 045/300: dt: 0.9000, rms radial error=170.555, avgs=0 050/300: dt: 0.9000, rms radial error=169.618, avgs=0 055/300: dt: 0.9000, rms radial error=168.684, avgs=0 060/300: dt: 0.9000, rms radial error=167.753, avgs=0 065/300: dt: 0.9000, rms radial error=166.825, avgs=0 070/300: dt: 0.9000, rms radial error=165.903, avgs=0 075/300: dt: 0.9000, rms radial error=164.984, avgs=0 080/300: dt: 0.9000, rms radial error=164.071, avgs=0 085/300: dt: 0.9000, rms radial error=163.162, avgs=0 090/300: dt: 0.9000, rms radial error=162.259, avgs=0 095/300: dt: 0.9000, rms radial error=161.360, avgs=0 100/300: dt: 0.9000, rms radial error=160.466, avgs=0 105/300: dt: 0.9000, rms radial error=159.576, avgs=0 110/300: dt: 0.9000, rms radial error=158.691, avgs=0 115/300: dt: 0.9000, rms radial error=157.810, avgs=0 120/300: dt: 0.9000, rms radial error=156.934, avgs=0 125/300: dt: 0.9000, rms radial error=156.062, avgs=0 130/300: dt: 0.9000, rms radial error=155.195, avgs=0 135/300: dt: 0.9000, rms radial error=154.333, avgs=0 140/300: dt: 0.9000, rms radial error=153.475, avgs=0 145/300: dt: 0.9000, rms radial error=152.622, avgs=0 150/300: dt: 0.9000, rms radial error=151.773, avgs=0 155/300: dt: 0.9000, rms radial error=150.929, avgs=0 160/300: dt: 0.9000, rms radial error=150.090, avgs=0 165/300: dt: 0.9000, rms radial error=149.255, avgs=0 170/300: dt: 0.9000, rms radial error=148.424, avgs=0 175/300: dt: 0.9000, rms radial error=147.598, avgs=0 180/300: dt: 0.9000, rms radial error=146.776, avgs=0 185/300: dt: 0.9000, rms radial error=145.958, avgs=0 190/300: dt: 0.9000, rms radial error=145.145, avgs=0 195/300: dt: 0.9000, rms radial error=144.337, avgs=0 200/300: dt: 0.9000, rms radial error=143.532, avgs=0 205/300: dt: 0.9000, rms radial error=142.733, avgs=0 210/300: dt: 0.9000, rms radial error=141.937, avgs=0 215/300: dt: 0.9000, rms radial error=141.146, avgs=0 220/300: dt: 0.9000, rms radial error=140.359, avgs=0 225/300: dt: 0.9000, rms radial error=139.576, avgs=0 230/300: dt: 0.9000, rms radial error=138.799, avgs=0 235/300: dt: 0.9000, rms radial error=138.025, avgs=0 240/300: dt: 0.9000, rms radial error=137.256, avgs=0 245/300: dt: 0.9000, rms radial error=136.490, avgs=0 250/300: dt: 0.9000, rms radial error=135.729, avgs=0 255/300: dt: 0.9000, rms radial error=134.973, avgs=0 260/300: dt: 0.9000, rms radial error=134.220, avgs=0 265/300: dt: 0.9000, rms radial error=133.472, avgs=0 270/300: dt: 0.9000, rms radial error=132.728, avgs=0 275/300: dt: 0.9000, rms radial error=131.988, avgs=0 280/300: dt: 0.9000, rms radial error=131.252, avgs=0 285/300: dt: 0.9000, rms radial error=130.520, avgs=0 290/300: dt: 0.9000, rms radial error=129.792, avgs=0 295/300: dt: 0.9000, rms radial error=129.068, avgs=0 300/300: dt: 0.9000, rms radial error=128.348, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 22045.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 4219.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00035 epoch 3 (K=160.0), pass 1, starting sse = 721.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00478 epoch 4 (K=640.0), pass 1, starting sse = 203.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/15 = 0.01155 final distance error %34.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 198.831256 mris_sphere stimesec 0.067999 mris_sphere ru_maxrss 237200 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 57732 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12728 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 818 FSRUNTIME@ mris_sphere 0.0553 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Mar 9 15:06:29 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Mar 9 15:06:29 -03 2020 /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Mar 9 15:06:29 -03 2020 mris_fix_topology -rusage /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 s13_msl3 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-944 (nv=188952, nf=379792, ne=569688, g=473) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 127091 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 22 defects to be corrected 0 vertices coincident reading input surface /home/lfa-03/Escritorio/Estudio_Flor/Primary_stream_with_secondary_stream_mask/s13_msl3/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7475 (-4.8738) -vertex loglikelihood: -6.7245 (-3.3623) -normal dot loglikelihood: -3.5267 (-3.5267) -quad curv loglikelihood: -5.8723 (-2.9361) Total Loglikelihood : -25.8710 CORRECTING DEFECT 0 (vertices=58037, convex hull=7267, v0=0)