mkbrainmask-sess sess01 $Id: mkbrainmask-sess,v 1.26 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sun Sep 30 01:22:50 EDT 2018 /media/sda1/nmrclass/tutorial_data/fsfast-functional /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -per-run -update ProjectDir /media/sda1/nmrclass/tutorial_data/fsfast-functional ------------------------------------------------ /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 Sun Sep 30 01:22:50 EDT 2018 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:51 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00268 -0.00300 0.72231; 0.00352 -0.22242 0.97494 -40.39471; -0.00195 0.97495 0.22243 -1.18300; 0.00000 0.00000 0.00000 1.00000; movvol template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538873989 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99999 0.00352 -0.00195 -0.58232; 0.00268 -0.22242 0.97495 -7.83319; -0.00300 0.97494 0.22243 39.64790; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43747 -0.00669 -0.01761 19.06136; -0.01032 0.76460 -4.87472 137.33600; -0.00921 -3.35138 -1.11210 244.38734; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24188 values in range Counting number of voxels in first frame Found 24188 voxels in final mask Count: 24188 1429076.079605 122880 19.684245 mri_binarize done Diliating 1 mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24188 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35032 voxels in final mask Count: 35032 2069761.585114 122880 28.509115 mri_binarize done Started at Sun Sep 30 01:22:51 EDT 2018 Ended at Sun Sep 30 01:22:52 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34360 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13946 voxels in final mask Count: 13946 823957.954613 122880 11.349284 mri_binarize done mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:53 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 001/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --inv --interp nearest --o 001/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 1.00000 -0.00051 -0.00113 0.57201; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36292; 0.00000 0.00000 0.00000 1.00000; movvol 001/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 001/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538978735 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00098 0.00076 -0.53141; -0.00051 -0.23948 0.97090 -8.38411; -0.00113 0.97090 0.23948 39.68396; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43750 0.00263 -0.00488 18.52054; -0.00389 0.82321 -4.85451 134.91533; 0.00175 -3.33747 -1.19740 244.32001; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 001/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24282 values in range Counting number of voxels in first frame Found 24282 voxels in final mask Count: 24282 1434629.790184 122880 19.760742 mri_binarize done Diliating 1 mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 001/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24282 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35036 voxels in final mask Count: 35036 2069997.913223 122880 28.512370 mri_binarize done Started at Sun Sep 30 01:22:53 EDT 2018 Ended at Sun Sep 30 01:22:54 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 001/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34360 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13936 voxels in final mask Count: 13936 823367.134338 122880 11.341146 mri_binarize done mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:55 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 002/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta --inv --interp nearest --o 002/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99998 -0.00250 0.00647 0.19577; -0.00689 -0.25597 0.96666 -40.69115; 0.00076 0.96668 0.25598 -1.83958; 0.00000 0.00000 0.00000 1.00000; movvol 002/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 002/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538829089 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99998 -0.00689 0.00076 -0.47481; -0.00250 -0.25597 0.96668 -8.63701; 0.00647 0.96666 0.25598 39.80412; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43742 0.00262 0.03446 17.87655; 0.02223 0.87994 -4.83330 131.82587; 0.00860 -3.32297 -1.27986 244.62051; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24283 values in range Counting number of voxels in first frame Found 24283 voxels in final mask Count: 24283 1434688.872211 122880 19.761556 mri_binarize done Diliating 1 mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24283 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35048 voxels in final mask Count: 35048 2070706.897552 122880 28.522135 mri_binarize done Started at Sun Sep 30 01:22:55 EDT 2018 Ended at Sun Sep 30 01:22:56 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 002/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34376 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13880 voxels in final mask Count: 13880 820058.540802 122880 11.295573 mri_binarize done mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:57 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 003/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99983 -0.01825 0.00009 -0.42357; -0.00480 -0.25833 0.96604 -41.01878; 0.01760 0.96588 0.25838 -1.98164; 0.00000 0.00000 0.00000 1.00000; movvol 003/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 003/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538757203 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99983 -0.00480 0.01760 0.26151; -0.01825 -0.25833 0.96588 -8.69022; 0.00009 0.96604 0.25838 40.13798; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43693 0.06051 0.02400 15.46057; 0.00030 0.88817 -4.83022 131.88400; 0.06272 -3.32022 -1.29167 242.92496; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24347 values in range Counting number of voxels in first frame Found 24347 voxels in final mask Count: 24347 1438470.121967 122880 19.813639 mri_binarize done Diliating 1 mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24347 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35050 voxels in final mask Count: 35050 2070825.061607 122880 28.523763 mri_binarize done Started at Sun Sep 30 01:22:57 EDT 2018 Ended at Sun Sep 30 01:22:58 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 003/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34362 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13952 voxels in final mask Count: 13952 824312.446777 122880 11.354167 mri_binarize done mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:59 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 004/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta --inv --interp nearest --o 004/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91511; 0.00000 0.00000 0.00000 1.00000; movvol 004/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 004/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538590017 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99969 -0.00187 0.02478 0.55637; -0.02448 -0.24691 0.96873 -8.29958; -0.00431 0.96904 0.24688 40.26850; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43644 0.08520 0.00933 14.61147; -0.01482 0.84864 -4.84518 133.72714; 0.08414 -3.33001 -1.23454 242.08621; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24267 values in range Counting number of voxels in first frame Found 24267 voxels in final mask Count: 24267 1433743.559772 122880 19.748535 mri_binarize done Diliating 1 mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24267 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 34978 voxels in final mask Count: 34978 2066571.155632 122880 28.465169 mri_binarize done Started at Sun Sep 30 01:22:59 EDT 2018 Ended at Sun Sep 30 01:23:00 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 004/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34288 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13871 voxels in final mask Count: 13871 819526.802555 122880 11.288249 mri_binarize done meanval --i 001/f.nii.gz --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat Sun Sep 30 01:23:00 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 001/f.nii.gz --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.29232/blah.29232 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.29232/blah.29232 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 001/masks/brain.e3.nii.gz Loading 001/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 001/global.meanval.dat 0 866.272 Writing to 001/global.waveform.dat mri_segstats done meanval --i 002/f.nii.gz --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat Sun Sep 30 01:23:02 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 002/f.nii.gz --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.29275/blah.29275 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.29275/blah.29275 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 002/masks/brain.e3.nii.gz Loading 002/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 002/global.meanval.dat 0 863.584 Writing to 002/global.waveform.dat mri_segstats done meanval --i 003/f.nii.gz --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat Sun Sep 30 01:23:03 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 003/f.nii.gz --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.29317/blah.29317 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.29317/blah.29317 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 003/masks/brain.e3.nii.gz Loading 003/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 003/global.meanval.dat 0 863.342 Writing to 003/global.waveform.dat mri_segstats done meanval --i 004/f.nii.gz --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat Sun Sep 30 01:23:05 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 004/f.nii.gz --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.29359/blah.29359 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.29359/blah.29359 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 004/masks/brain.e3.nii.gz Loading 004/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 004/global.meanval.dat 0 864.522 Writing to 004/global.waveform.dat mri_segstats done Sun Sep 30 01:23:06 EDT 2018 mkbrainmask-sess done