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Hello again: I have downloaded this raw data from a database that’s the reason I’m not sure it is T1w but I think what they call ntdi it is. So when I run recon-all from this ntdi.nifti file it gives me a Talairach error.
I send you the output terminal.
Sun Aug 5 21:16:32 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi /Applications/freesurfer/bin/recon-all -all -i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz -s Parkinson_p06316_ntdi subjid Parkinson_p06316_ntdi setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709
PhysMem: 6923M used (1652M wired), 1269M unused.
######################################## program versions used $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /Applications/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 /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz \n mri_convert.bin /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Aug 5 21:16:37 -05 2018 Found 1 runs /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/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. \n cp /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform \n mri_convert.bin /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach.xfm /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Aug 5 21:16:45 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:16:45 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.28472 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28472/nu0.mnc...
-------------------------------------------------------- Iteration 1 Sun Aug 5 21:16:48 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28472/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:16:48] running: /Applications/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.28472/0/ ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.28472/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.28472/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.28472/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:17:50 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:17:51 -05 2018 Ended at Sun Aug 5 21:18:23 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5625, pval=0.2115 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82155 z-score: -35 WARNING: Talairach QA check failed! z-score of -35 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Retrying Talairach align using 3T-based atlas...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:18:25 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.29321 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29321/nu0.mnc...
-------------------------------------------------------- Iteration 1 Sun Aug 5 21:18:29 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29321/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:18:29] running: /Applications/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.29321/0/ ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.29321/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.29321/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.29321/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:19:31 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:19:32 -05 2018 Ended at Sun Aug 5 21:20:06 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6718, pval=0.3663 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82839 z-score: -34 WARNING: Talairach QA check failed! z-score of -34 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Trying MINC mritotal to perform Talairach align...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:20:09 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.30729 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30729/nu0.mnc...
-------------------------------------------------------- Iteration 1 Sun Aug 5 21:20:14 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30729/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:20:14] running: /Applications/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.30729/0/ ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.30729/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.30729/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.30729/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:21:38 -05 2018 mri_nu_correct.mni done \n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:21:38 -05 2018 tmpdir is transforms/tmp.talairach.31560 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig_nu.mgz transforms/tmp.talairach.31560/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.31560/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.31560/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.31560/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 116.684 Source min/max voxel= -0.000 116.684
Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710
AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -0.3191 0.0000 1.0000 0.0000 4.1855 0.0000 0.0000 1.0000 -2.5422
Transform center = 0.647 -21.776 11.997 Transform rotations = 0.000 0.000 0.000 Transform trans = -0.319 4.185 -2.542 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 77.500 -58.500 83.500 Lattice count = 40 38 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 174.918 Source min/max voxel= -0.000 174.918
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070
AFTER init_params() Transform matrix = 1.4213 -0.0312 0.0250 -0.2569 0.0206 1.3338 0.4922 11.6646 -0.0342 -0.4917 1.3337 -18.5176
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.353 0.024 0.014 Transform trans = 0.994 10.314 -3.829 Transform scale = 1.422 1.422 1.422 Transform shear = -0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 71.500 -68.500 77.500 Lattice count = 36 35 35
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.4372 -0.0374 0.0061 -0.2060 0.0338 1.3698 0.4353 11.2444 -0.0171 -0.4350 1.3702 -17.4590
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.307 0.012 0.023 Transform trans = 0.963 8.436 -3.557 Transform scale = 1.438 1.438 1.438 Transform shear = -0.000 0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6144 -0.2750 0.5425 -14.4883 0.0458 1.5894 0.6694 16.3050 -0.6065 -0.6120 1.4946 -40.0914
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.389 0.359 0.028 Transform trans = -1.593 11.531 -21.224 Transform scale = 1.725 1.725 1.725 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6312 -0.3050 0.7870 -20.1748 -0.0181 1.4680 0.6063 8.4898 -0.7867 -0.5889 1.4024 -45.8197
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.398 0.477 -0.013 Transform trans = -3.684 5.561 -28.676 Transform scale = 1.837 1.588 1.712 Transform shear = 0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.5355 -0.3201 0.8187 -21.3346 -0.0758 1.4582 0.7124 7.0942 -1.0405 -0.8460 1.6208 -52.7173
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.481 0.517 -0.054 Transform trans = -4.196 5.614 -27.520 Transform scale = 1.769 1.625 2.104 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Sun Aug 5 21:21:53 -05 2018 talairach done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:21:56 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0001, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
\nERROR: Talairach failed!\n Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
recon-all -s Parkinson_p06316_ntdi exited with ERRORS at Sun Aug 5 21:21:56 -05 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
You should first verify that the input is in fact a T1 of about 1mm resolution and that there are no obvious artifacts. After that, you should check the talairach registration (see the web page it points you to)
On 08/06/2018 04:40 PM, Renew Andrade wrote:
External Email - Use CautionHello again: I have downloaded this raw data from a database that’s the reason I’m not sure it is T1w but I think what they call ntdi it is. So when I run recon-all from this ntdi.nifti file it gives me a Talairach error.
I send you the output terminal.
Sun Aug 5 21:16:32 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi /Applications/freesurfer/bin/recon-all -all -i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz -s Parkinson_p06316_ntdi subjid Parkinson_p06316_ntdi setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709
PhysMem: 6923M used (1652M wired), 1269M unused.
######################################## program versions used $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /Applications/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 /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz \n mri_convert.bin /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Aug 5 21:16:37 -05 2018 Found 1 runs /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/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. \n cp /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform \n mri_convert.bin /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach.xfm /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Aug 5 21:16:45 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:16:45 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.28472 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28472/nu0.mnc...
Iteration 1 Sun Aug 5 21:16:48 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28472/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:16:48] running: /Applications/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.28472/0/ ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.28472/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.28472/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.28472/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:17:50 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:17:51 -05 2018 Ended at Sun Aug 5 21:18:23 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5625, pval=0.2115 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82155 z-score: -35 WARNING: Talairach QA check failed! z-score of -35 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Retrying Talairach align using 3T-based atlas...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:18:25 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.29321 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29321/nu0.mnc...
Iteration 1 Sun Aug 5 21:18:29 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29321/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:18:29] running: /Applications/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.29321/0/ ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.29321/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.29321/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.29321/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:19:31 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:19:32 -05 2018 Ended at Sun Aug 5 21:20:06 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6718, pval=0.3663 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82839 z-score: -34 WARNING: Talairach QA check failed! z-score of -34 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Trying MINC mritotal to perform Talairach align...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:20:09 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.30729 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30729/nu0.mnc...
Iteration 1 Sun Aug 5 21:20:14 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30729/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:20:14] running: /Applications/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.30729/0/ ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.30729/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.30729/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.30729/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:21:38 -05 2018 mri_nu_correct.mni done \n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:21:38 -05 2018 tmpdir is transforms/tmp.talairach.31560 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig_nu.mgz transforms/tmp.talairach.31560/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.31560/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.31560/src.mnc...
mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.31560/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 116.684 Source min/max voxel= -0.000 116.684
Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710
AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -0.3191 0.0000 1.0000 0.0000 4.1855 0.0000 0.0000 1.0000 -2.5422
Transform center = 0.647 -21.776 11.997 Transform rotations = 0.000 0.000 0.000 Transform trans = -0.319 4.185 -2.542 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 77.500 -58.500 83.500 Lattice count = 40 38 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 174.918 Source min/max voxel= -0.000 174.918
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070
AFTER init_params() Transform matrix = 1.4213 -0.0312 0.0250 -0.2569 0.0206 1.3338 0.4922 11.6646 -0.0342 -0.4917 1.3337 -18.5176
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.353 0.024 0.014 Transform trans = 0.994 10.314 -3.829 Transform scale = 1.422 1.422 1.422 Transform shear = -0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 71.500 -68.500 77.500 Lattice count = 36 35 35
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.4372 -0.0374 0.0061 -0.2060 0.0338 1.3698 0.4353 11.2444 -0.0171 -0.4350 1.3702 -17.4590
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.307 0.012 0.023 Transform trans = 0.963 8.436 -3.557 Transform scale = 1.438 1.438 1.438 Transform shear = -0.000 0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6144 -0.2750 0.5425 -14.4883 0.0458 1.5894 0.6694 16.3050 -0.6065 -0.6120 1.4946 -40.0914
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.389 0.359 0.028 Transform trans = -1.593 11.531 -21.224 Transform scale = 1.725 1.725 1.725 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6312 -0.3050 0.7870 -20.1748 -0.0181 1.4680 0.6063 8.4898 -0.7867 -0.5889 1.4024 -45.8197
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.398 0.477 -0.013 Transform trans = -3.684 5.561 -28.676 Transform scale = 1.837 1.588 1.712 Transform shear = 0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.5355 -0.3201 0.8187 -21.3346 -0.0758 1.4582 0.7124 7.0942 -1.0405 -0.8460 1.6208 -52.7173
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.481 0.517 -0.054 Transform trans = -4.196 5.614 -27.520 Transform scale = 1.769 1.625 2.104 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Sun Aug 5 21:21:53 -05 2018 talairach done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:21:56 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0001, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
\nERROR: Talairach failed!\n Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
recon-all -s Parkinson_p06316_ntdi exited with ERRORS at Sun Aug 5 21:21:56 -05 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and make sure that the direction cosines are correct (that is, the directions that freeview says are in fact the actual anatomical directions)
On Mon, 6 Aug 2018, Douglas N. Greve wrote:
You should first verify that the input is in fact a T1 of about 1mm resolution and that there are no obvious artifacts. After that, you should check the talairach registration (see the web page it points you to)
On 08/06/2018 04:40 PM, Renew Andrade wrote:
External Email - Use CautionHello again: I have downloaded this raw data from a database that’s the reason I’m not sure it is T1w but I think what they call ntdi it is. So when I run recon-all from this ntdi.nifti file it gives me a Talairach error.
I send you the output terminal.
Sun Aug 5 21:16:32 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi /Applications/freesurfer/bin/recon-all -all -i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz -s Parkinson_p06316_ntdi subjid Parkinson_p06316_ntdi setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709
PhysMem: 6923M used (1652M wired), 1269M unused.
######################################## program versions used $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:33-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/08/06-02:16:34-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: andraderenew Machine: Renes-MacBook-Air-2.local Platform: Darwin PlatformVersion: 17.5.0 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /Applications/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 /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz \n mri_convert.bin /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Aug 5 21:16:37 -05 2018 Found 1 runs /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/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. \n cp /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig/001.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi \n mri_convert /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform \n mri_convert.bin /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach.xfm /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Aug 5 21:16:45 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:16:45 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.28472 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28472/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28472/nu0.mnc...
Iteration 1 Sun Aug 5 21:16:48 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28472/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:16:48] running: /Applications/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.28472/0/ ./tmp.mri_nu_correct.mni.28472/nu0.mnc ./tmp.mri_nu_correct.mni.28472/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.28472/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.28472/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.28472/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:17:50 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:17:51 -05 2018 Ended at Sun Aug 5 21:18:23 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5625, pval=0.2115 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82155 z-score: -35 WARNING: Talairach QA check failed! z-score of -35 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Retrying Talairach align using 3T-based atlas...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:18:25 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:18:25 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.29321 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29321/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.29321/nu0.mnc...
Iteration 1 Sun Aug 5 21:18:29 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29321/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:18:29] running: /Applications/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.29321/0/ ./tmp.mri_nu_correct.mni.29321/nu0.mnc ./tmp.mri_nu_correct.mni.29321/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.29321/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.29321/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.29321/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:19:31 -05 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig \n talairach_avi log file is transforms/talairach_avi.log... Started at Sun Aug 5 21:19:32 -05 2018 Ended at Sun Aug 5 21:20:06 -05 2018 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6718, pval=0.3663 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/transforms/talairach_avi.log \n TalAviQA: 0.82839 z-score: -34 WARNING: Talairach QA check failed! z-score of -34 is <= threshold of -9\n \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Trying MINC mritotal to perform Talairach align...\n #-------------------------------------------- #@# Talairach Sun Aug 5 21:20:09 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/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: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:20:09 -05 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.30729 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30729/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30729/nu0.mnc...
Iteration 1 Sun Aug 5 21:20:14 -05 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30729/0/ -iterations 1000 -distance 50 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri/] [2018-08-05 21:20:14] running: /Applications/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.30729/0/ ./tmp.mri_nu_correct.mni.30729/nu0.mnc ./tmp.mri_nu_correct.mni.30729/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 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: 35 CV of field change: 0.000959086
mri_convert ./tmp.mri_nu_correct.mni.30729/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.30729/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.30729/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz...
Sun Aug 5 21:21:38 -05 2018 mri_nu_correct.mni done \n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri /Applications/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Sun Aug 5 21:21:38 -05 2018 tmpdir is transforms/tmp.talairach.31560 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri mri_convert orig_nu.mgz transforms/tmp.talairach.31560/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.31560/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.31560/src.mnc...
mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.31560/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 116.684 Source min/max voxel= -0.000 116.684
Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710
AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -0.3191 0.0000 1.0000 0.0000 4.1855 0.0000 0.0000 1.0000 -2.5422
Transform center = 0.647 -21.776 11.997 Transform rotations = 0.000 0.000 0.000 Transform trans = -0.319 4.185 -2.542 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 77.500 -58.500 83.500 Lattice count = 40 38 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 174.918 Source min/max voxel= -0.000 174.918
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070
AFTER init_params() Transform matrix = 1.4213 -0.0312 0.0250 -0.2569 0.0206 1.3338 0.4922 11.6646 -0.0342 -0.4917 1.3337 -18.5176
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.353 0.024 0.014 Transform trans = 0.994 10.314 -3.829 Transform scale = 1.422 1.422 1.422 Transform shear = -0.000 0.000 0.000
Source volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = 71.500 -68.500 77.500 Lattice count = 36 35 35
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.4372 -0.0374 0.0061 -0.2060 0.0338 1.3698 0.4353 11.2444 -0.0171 -0.4350 1.3702 -17.4590
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.307 0.012 0.023 Transform trans = 0.963 8.436 -3.557 Transform scale = 1.438 1.438 1.438 Transform shear = -0.000 0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6144 -0.2750 0.5425 -14.4883 0.0458 1.5894 0.6694 16.3050 -0.6065 -0.6120 1.4946 -40.0914
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.389 0.359 0.028 Transform trans = -1.593 11.531 -21.224 Transform scale = 1.725 1.725 1.725 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.6312 -0.3050 0.7870 -20.1748 -0.0181 1.4680 0.6063 8.4898 -0.7867 -0.5889 1.4024 -45.8197
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.398 0.477 -0.013 Transform trans = -3.684 5.561 -28.676 Transform scale = 1.837 1.588 1.712 Transform shear = 0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.052 20.198 Source min/max voxel= 0.052 20.198
Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652
AFTER init_params() Transform matrix = 1.5355 -0.3201 0.8187 -21.3346 -0.0758 1.4582 0.7124 7.0942 -1.0405 -0.8460 1.6208 -52.7173
Transform center = 0.647 -21.776 11.997 Transform rotations = -0.481 0.517 -0.054 Transform trans = -4.196 5.614 -27.520 Transform scale = 1.769 1.625 2.104 Transform shear = -0.000 -0.000 0.000
Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34
Sun Aug 5 21:21:53 -05 2018 talairach done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 5 21:21:56 -05 2018 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0001, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
\nERROR: Talairach failed!\n Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
recon-all -s Parkinson_p06316_ntdi exited with ERRORS at Sun Aug 5 21:21:56 -05 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N. Greve -
Renew Andrade