/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Tue May 25 17:35:13 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.234948 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.234948/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.234948/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.234948/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Tue May 25 17:35:29 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.234948/nu0.mnc ./tmp.mri_nu_correct.mni.234948/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.234948/0/ [bpinsard@blg8112.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/] [2021-05-25 17:35:29] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.234948/0/ ./tmp.mri_nu_correct.mni.234948/nu0.mnc ./tmp.mri_nu_correct.mni.234948/nu1.imp Processing:.................................................................................Done 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Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Tue May 25 17:37:31 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.234948/nu1.mnc ./tmp.mri_nu_correct.mni.234948/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.234948/1/ [bpinsard@blg8112.int.ets1.calculquebec.ca:/lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/] [2021-05-25 17:37:31] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.234948/1/ ./tmp.mri_nu_correct.mni.234948/nu1.mnc ./tmp.mri_nu_correct.mni.234948/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done 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Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.234948/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.234948/ones.mgz sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard input ./tmp.mri_nu_correct.mni.234948/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.234948/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 32768000 values in range Counting number of voxels in first frame Found 32768000 voxels in final mask Count: 32768000 16777212.890625 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.234948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.234948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/input.mean.dat sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.234948/ones.mgz Loading orig.mgz Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.234948/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.234948/ones.mgz --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.234948/ones.mgz --i ./tmp.mri_nu_correct.mni.234948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.234948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.234948/output.mean.dat sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Loading ./tmp.mri_nu_correct.mni.234948/ones.mgz Loading ./tmp.mri_nu_correct.mni.234948/nu2.mnc Voxel Volume is 0.512 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.234948/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.234948/nu2.mnc ./tmp.mri_nu_correct.mni.234948/nu2.mnc mul .91770764551582458463 mri_convert ./tmp.mri_nu_correct.mni.234948/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.234948/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.234948/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 10 seconds. mapping ( 8, 165) to ( 3, 110) Tue May 25 17:40:33 UTC 2021 mri_nu_correct.mni done