nu_reference_1 fails with develop and 1.9.18-devel

[gdevenyi]

UpdateCTestConfiguration  from :/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/DartConfiguration.tcl
UpdateCTestConfiguration  from :/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/DartConfiguration.tcl
Test project /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 18
    Start 18: nu_reference_1

18: Test command: /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/compare_nu_result.pl "/home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz" "-mask" "/home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz" "/home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain_nu_ref.mnc.gz" "0.0001" "--verbose"
18: Environment variables: 
18:  PATH=/home/gdevenyi/projects/software/minc-toolkit-v2-build:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3:/home/gdevenyi/projects/software/minc-toolkit-v2-build/classify:/home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs:/home/gdevenyi/projects/software/minc-toolkit-v2-build/mni_autoreg/mincblur:/home/gdevenyi/projects/software/minc-toolkit-v2-build/mni_autoreg/make_phantom:/home/gdevenyi/projects/software/minc-toolkit-v2-build/mni_autoreg/minctracc:/home/gdevenyi/projects/software/minc-toolkit-v2-build/external//home/gdevenyi/quarantine/bin:/usr/lib/ccache:/home/gdevenyi/bin:/home/gdevenyi/.dotfiles/bin:/home/gdevenyi/bin:/home/gdevenyi/miniforge3/condabin:/usr/lib/ccache:/home/gdevenyi/bin:/home/gdevenyi/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
18:  PERL5LIB=/home/gdevenyi/projects/software/minc-toolkit-v2/mni-perllib:/home/gdevenyi/projects/software/minc-toolkit-v2-build/mni-perllib/perl:/home/gdevenyi/projects/software/minc-toolkit-v2-build/perl-modules:
18:  LD_LIBRARY_PATH=/home/gdevenyi/projects/software/minc-toolkit-v2-build/external//home/gdevenyi/quarantine/lib:/home/gdevenyi/projects/software/minc-toolkit-v2-build/libminc:/home/gdevenyi/projects/software/minc-toolkit-v2-build/libminc/ezminc:
18: Test timeout computed to be: 10000000
18: nu_estimate /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp -mask /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz -verbose
18: [nu_estimate] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:18] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -mask /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz -verbose -execute -noclobber -nokeeptmp -tmpdir /var/tmp/nu_estimate_39462/ /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp
18: Warning: Cannot read average brain mask: /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
18: 
18: Uncorrected volume (input): /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz
18: Intensity mapping (output): /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp
18: 
18: # Start of NU estimation algorithm
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:18] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincresample -clobber -verbose -nearest_neighbour -nelements 24 28 24 -step 8 8 8 /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /var/tmp/nu_estimate_39462/brain.mnc
18: Transforming slices:........................Done
18: Resampling /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz like /var/tmp/nu_estimate_39462/brain.mnc
18: 
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:18] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/resample_labels -clobber -verbose -resample '-like /var/tmp/nu_estimate_39462/brain.mnc' /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp
18: [resample_labels] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:18] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincresample /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/../model_data/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /var/tmp/resample_labels_39471/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -trilinear -byte  -like /var/tmp/nu_estimate_39462/brain.mnc 
18: Transforming slices:........................Done
18: [resample_labels] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/extracttag /var/tmp/resample_labels_39471/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -volume /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp -threshold 0.5 1.1 -label 1 -maxtags 0
18: Updating history
18: Elapsed time in resample_labels (39471) and children:
18: 0.22 sec (user) + 0.05 sec (system) = 0.27 sec (total)
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincresample -clobber -verbose -like /var/tmp/nu_estimate_39462/brain.mnc /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
18: Transforming slices:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/rm /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -clamp -const2 1 1.7e+308 /var/tmp/nu_estimate_39462/brain.mnc /var/tmp/nu_estimate_39462/brain_log.mnc.temp
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -zero -log /var/tmp/nu_estimate_39462/brain_log.mnc.temp /var/tmp/nu_estimate_39462/brain_log.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/rm /var/tmp/nu_estimate_39462/brain_log.mnc.temp
18: # thresholding background
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -short -zero -gt -const 1 /var/tmp/nu_estimate_39462/brain.mnc /var/tmp/nu_estimate_39462/brain_bkg.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_bkg.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -short -signed -and /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc /var/tmp/nu_estimate_39462/brain_bkg.mnc /var/tmp/nu_estimate_39462/brain_mask.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_bkg.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/rm /var/tmp/nu_estimate_39462/brain_bkg.mnc
18: # apply mask to log volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult -zero /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_mask.mnc.temp
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/mv /var/tmp/nu_estimate_39462/brain_mask.mnc.temp /var/tmp/nu_estimate_39462/brain_log.mnc
18: # create flat initial field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -short -mult -const 0 /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: Processing:........................Done
18: 
18: # Starting iteration 0
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 9.985434 13.341061 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 9.985434 13.341061 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 0: 0.00979095
18: 
18: 
18: # Starting iteration 1
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 9.996244 13.320735 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 9.996244 13.320735 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 1: 0.00863781
18: 
18: 
18: # Starting iteration 2
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.008431 13.306663 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.008431 13.306663 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:19] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 2: 0.00748988
18: 
18: 
18: # Starting iteration 3
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.023108 13.295959 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.023108 13.295959 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 3: 0.00666054
18: 
18: 
18: # Starting iteration 4
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.033246 13.287886 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.033246 13.287886 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 4: 0.00582972
18: 
18: 
18: # Starting iteration 5
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.045146 13.282167 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.045146 13.282167 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 5: 0.00526725
18: 
18: 
18: # Starting iteration 6
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.059375 13.283825 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.059375 13.283825 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 6: 0.00471576
18: 
18: 
18: # Starting iteration 7
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:20] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.070152 13.289486 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.070152 13.289486 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 7: 0.00419457
18: 
18: 
18: # Starting iteration 8
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.080967 13.295189 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.080967 13.295189 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 8: 0.00388341
18: 
18: 
18: # Starting iteration 9
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.091655 13.300717 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.091655 13.300717 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 9: 0.00352152
18: 
18: 
18: # Starting iteration 10
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.099099 13.306245 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.099099 13.306245 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 10: 0.00336202
18: 
18: 
18: # Starting iteration 11
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.106306 13.311458 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.106306 13.311458 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:21] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 11: 0.00314993
18: 
18: 
18: # Starting iteration 12
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.116769 13.316672 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.116769 13.316672 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 12: 0.00299922
18: 
18: 
18: # Starting iteration 13
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.120639 13.321766 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.120639 13.321766 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 13: 0.00288151
18: 
18: 
18: # Starting iteration 14
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.130954 13.326776 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.130954 13.326776 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 14: 0.00277242
18: 
18: 
18: # Starting iteration 15
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.137855 13.331573 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.137855 13.331573 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 15: 0.00261681
18: 
18: 
18: # Starting iteration 16
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.141317 13.336125 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.141317 13.336125 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 16: 0.00250935
18: 
18: 
18: # Starting iteration 17
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:22] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.148831 13.341722 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.148831 13.341722 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 17: 0.00239733
18: 
18: 
18: # Starting iteration 18
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.154131 13.348688 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.154131 13.348688 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 18: 0.00221773
18: 
18: 
18: # Starting iteration 19
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.162437 13.355320 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.162437 13.355320 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 19: 0.00211654
18: 
18: 
18: # Starting iteration 20
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.173650 13.361480 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.173650 13.361480 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 20: 0.00192124
18: 
18: 
18: # Starting iteration 21
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.178071 13.367287 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.178071 13.367287 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 21: 0.0017709
18: 
18: 
18: # Starting iteration 22
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.185630 13.372925 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.185630 13.372925 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:23] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 22: 0.00172797
18: 
18: 
18: # Starting iteration 23
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.189689 13.378254 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.189689 13.378254 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 23: 0.00157644
18: 
18: 
18: # Starting iteration 24
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.193486 13.383240 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.193486 13.383240 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 24: 0.00146777
18: 
18: 
18: # Starting iteration 25
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.203633 13.387977 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.203633 13.387977 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 25: 0.00137817
18: 
18: 
18: # Starting iteration 26
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.210557 13.392770 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.210557 13.392770 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 26: 0.00124301
18: 
18: 
18: # Starting iteration 27
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.214296 13.397675 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.214296 13.397675 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 27: 0.00122875
18: 
18: 
18: # Starting iteration 28
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:24] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.224274 13.402178 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.224274 13.402178 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 28: 0.0011794
18: 
18: 
18: # Starting iteration 29
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.227633 13.406581 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.227633 13.406581 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 29: 0.00107701
18: 
18: 
18: # Starting iteration 30
18: # correct volume using field estimate
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_corr.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_corr.mnc
18: Processing:........................Done
18: # compute residual volume from classification of corrected volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/cp /var/tmp/nu_estimate_39462/brain_corr.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_volume -clobber -verbose -parzen -bins 200 -fwhm 0.15 -noise 0.01 /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/volume_hist -bins 200 -auto_range -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.hist -clobber -text -select 1 -quiet -window
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/sharpen_hist -clobber -fwhm 0.15 -noise 0.01 -quiet -range 10.231096 13.411119 /var/tmp/nu_estimate_39462/brain_est.hist /var/tmp/nu_estimate_39462/brain_est.sharp
18: [sharpen_volume] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minclookup -continuous -range 10.231096 13.411119 -clobber -lookup_table /var/tmp/nu_estimate_39462/brain_est.sharp /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -mult /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_est.mnc.temp /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_mask.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc.temp
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub /var/tmp/nu_estimate_39462/brain_log.mnc /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_log.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_est.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_est.mnc
18: # filter residue volume
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -sub -zero /var/tmp/nu_estimate_39462/brain_est.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_est.mnc
18:  | [01]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_temp.mnc
18: Processing:........................Done
18: CV for change in field estimate at iteration 30: 0.000999069
18: 
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -zero -exp /var/tmp/nu_estimate_39462/brain_residue.mnc /var/tmp/nu_estimate_39462/brain_residue.mnc.temp
18: 
18: +++ infiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_residue.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /var/tmp/nu_estimate_39462/brain_residue.mnc.temp
18: Processing:........................Done
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /bin/mv /var/tmp/nu_estimate_39462/brain_residue.mnc.temp /var/tmp/nu_estimate_39462/brain_temp.mnc
18: [nu_estimate_np_and_em] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/spline_smooth -clobber -verbose -full_support -distance 200 -b_spline -lambda 1.0e-7 -subsample 1 -novolume -mask /var/tmp/nu_estimate_39462/brain_mask.mnc /var/tmp/nu_estimate_39462/brain_temp.mnc -compact /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp
18: Number of iterations: 31 
18: CV of field change: 0.000999069
18: # NU estimation complete.
18: nu_evaluate /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz -mapping /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp /tmp/compare_nu_result.pl-6nPaIJr1/brain_nu.mnc -verbose
18: [nu_evaluate] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/minccalc -clobber -verbose -quiet -byte -expression 'if(A[0]>=241926.3418
18: ){out=1}else{out=0}' /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /var/tmp/nu_evaluate_39875//nuc_auto_mask.mnc
18: [nu_evaluate] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:25] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/evaluate_field -clobber -verbose -mask /var/tmp/nu_evaluate_39875//nuc_auto_mask.mnc -like /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /tmp/compare_nu_result.pl-6nPaIJr1/brain.imp /var/tmp/nu_evaluate_39875//brain_nu_field.mnc
18: [nu_evaluate] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:26] /home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/correct_field /var/tmp/nu_evaluate_39875//brain_nu_field.mnc /var/tmp/nu_evaluate_39875//nuc_auto_mask.mnc /var/tmp/nu_evaluate_39875//brain_nu_field.mnc
18: [nu_evaluate] [:/home/gdevenyi/projects/software/minc-toolkit-v2-build/N3/testing] [2020-07-17 17:03:27] /home/gdevenyi/projects/software/minc-toolkit-v2-build/minctools/progs/mincmath -clobber -verbose -copy_header -zero -div /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz /var/tmp/nu_evaluate_39875//brain_nu_field.mnc /tmp/compare_nu_result.pl-6nPaIJr1/brain_nu.mnc
18: 
18: +++ infiles +++
18:  | [00]: /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain.mnc.gz
18:  | [01]: /var/tmp/nu_evaluate_39875//brain_nu_field.mnc
18: 
18: +++ outfiles +++
18:  | [00]: /tmp/compare_nu_result.pl-6nPaIJr1/brain_nu.mnc
18: Processing:...........................................................................................Done
18: mincmath -sub -float /tmp/compare_nu_result.pl-6nPaIJr1/brain_nu.mnc /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain_nu_ref.mnc.gz /tmp/compare_nu_result.pl-6nPaIJr1/diff.mnc
18: 
18: +++ infiles +++
18:  | [00]: /tmp/compare_nu_result.pl-6nPaIJr1/brain_nu.mnc
18:  | [01]: /home/gdevenyi/projects/software/minc-toolkit-v2/N3/testing/brain_nu_ref.mnc.gz
18: 
18: +++ outfiles +++
18:  | [00]: /tmp/compare_nu_result.pl-6nPaIJr1/diff.mnc
18: Processing:...........................................................................................Done
18: relative RMS difference: 0.00477038445899682 larger then 0.0001
1/1 Test #18: nu_reference_1 ...................***Failed    9.46 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   9.46 sec

The following tests FAILED:
	 18 - nu_reference_1 (Failed)