dHCP Segmentation pipeline T2: /data/workdir/sub-NYS1553-ses-001/T2/sub-NYS1553-ses-001.nii.gz Subject: sub-NYS1553-ses-001 Age: 43 Directory: /data/workdir/sub-NYS1553-ses-001 Threads: 8 /usr/src/structural-pipeline/scripts/segmentation/pipeline.sh /data/workdir/sub-NYS1553-ses-001/T2/sub-NYS1553-ses-001.nii.gz sub-NYS1553-ses-001 43 -d /data/workdir/sub-NYS1553-ses-001 -t 8 ---------------------------- mirtk neonatal-segmentation /data/workdir/sub-NYS1553-ses-001/T2/sub-NYS1553-ses-001.nii.gz 43 -t 8 -c 1 -p 1 -v 1 -atlas non-rigid-v2 DrawEM multi atlas (HEAD (branch version: e6e1c2ab6f8a8c01a4a82e3d0a71b224e42a8e73) Subject: sub-NYS1553-ses-001 Age: 43 Directory: /data/workdir/sub-NYS1553-ses-001 Posteriors: 1 Cleanup: 1 Threads: 8 /usr/src/structural-pipeline/build/MIRTK/build/lib/tools/neonatal-segmentation /data/workdir/sub-NYS1553-ses-001/T2/sub-NYS1553-ses-001.nii.gz 43 -t 8 -c 1 -p 1 -v 1 -atlas non-rigid-v2 ---------------------------- preprocess.sh sub-NYS1553-ses-001 mirtk convert-image T2/sub-NYS1553-ses-001.nii.gz N4/sub-NYS1553-ses-001_rescaled.nii.gz -rescale 0 1000 -double bet N4/sub-NYS1553-ses-001_rescaled.nii.gz segmentations/sub-NYS1553-ses-001_brain.nii.gz -R -f 0.1 -m mirtk N4 3 -i N4/sub-NYS1553-ses-001_rescaled.nii.gz -x segmentations/sub-NYS1553-ses-001_brain_mask.nii.gz -o [N4/sub-NYS1553-ses-001_corr.nii.gz,bias/sub-NYS1553-ses-001.nii.gz] -c [50x50x50,0.001] -s 2 -b [100,3] -t [0.15,0.01,200] mirtk calculate N4/sub-NYS1553-ses-001_corr.nii.gz -mul segmentations/sub-NYS1553-ses-001_brain_mask.nii.gz -out N4/sub-NYS1553-ses-001_corr.nii.gz mirtk convert-image N4/sub-NYS1553-ses-001_corr.nii.gz N4/sub-NYS1553-ses-001.nii.gz -rescale 0 1000 -double tissue-priors.sh sub-NYS1553-ses-001 43 non-rigid-v2 8 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/T2/template-43.nii.gz -dofout dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg.cfg -threads 8 -v 0 creating sub-NYS1553-ses-001 tissue priors mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure1/43.nii.gz segmentations-data/template/csf/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure2/43.nii.gz segmentations-data/template/gm/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure3/43.nii.gz segmentations-data/template/wm/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure4/43.nii.gz segmentations-data/template/outlier/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure5/43.nii.gz segmentations-data/template/ventricles/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure6/43.nii.gz segmentations-data/template/cerebstem/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure7/43.nii.gz segmentations-data/template/dgm/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure8/43.nii.gz segmentations-data/template/hwm/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/non-rigid-v2/atlas-9/structure9/43.nii.gz segmentations-data/template/lwm/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target N4/sub-NYS1553-ses-001.nii.gz -interp Linear mirtk calculate segmentations-data/tissue-posteriors/gm/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz register-multi-atlas-using-gm-posteriors.sh sub-NYS1553-ses-001 43 8 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_01.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_01.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_01-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_02.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_02.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_02-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_03.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_03.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_03-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_04.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_04.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_04-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_05.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_05.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_05-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_06.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_06.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_06-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_07.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_07.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_07-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_08.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_08.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_08-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_09.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_09.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_09-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_10.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_10.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_10-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_11.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_11.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_11-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_12.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_12.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_12-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_13.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_13.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_13-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_14.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_14.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_14-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_15.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_15.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_15-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_16.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_16.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_16-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_17.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_17.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_17-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_18.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_18.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_18-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_19.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_19.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_19-n.dof.gz -threads 8 -v 0 mirtk register N4/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_20.nii.gz segmentations-data/gm-posteriors/sub-NYS1553-ses-001.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/gm-posteriors-v3/ALBERT_20.nii.gz -parin /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/ireg-multichannel-structural.cfg -dofout dofs/sub-NYS1553-ses-001-ALBERT_20-n.dof.gz -threads 8 -v 0 labels-multi-atlas.sh sub-NYS1553-ses-001 mirtk convert-image N4/sub-NYS1553-ses-001.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -rescale 0 200 -double mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_01.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_01.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_01-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_01.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_01.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_01-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_01.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_01.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_01-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_01.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_02.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_02.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_02-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_02.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_02.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_02-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_02.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_02.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_02-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_02.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_03.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_03.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_03-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_03.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_03.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_03-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_03.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_03.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_03-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_03.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_04.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_04.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_04-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_04.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_04.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_04-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_04.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_04.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_04-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_04.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_05.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_05.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_05-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_05.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_05.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_05-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_05.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_05.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_05-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_05.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_06.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_06.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_06-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_06.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_06.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_06-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_06.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_06.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_06-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_06.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_07.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_07.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_07-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_07.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_07.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_07-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_07.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_07.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_07-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_07.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_08.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_08.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_08-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_08.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_08.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_08-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_08.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_08.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_08-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_08.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_09.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_09.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_09-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_09.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_09.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_09-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_09.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_09.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_09-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_09.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_10.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_10.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_10-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_10.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_10.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_10-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_10.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_10.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_10-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_10.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_11.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_11.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_11-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_11.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_11.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_11-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_11.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_11.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_11-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_11.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_12.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_12.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_12-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_12.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_12.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_12-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_12.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_12.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_12-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_12.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_13.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_13.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_13-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_13.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_13.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_13-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_13.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_13.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_13-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_13.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_14.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_14.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_14-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_14.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_14.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_14-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_14.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_14.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_14-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_14.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_15.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_15.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_15-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_15.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_15.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_15-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_15.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_15.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_15-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_15.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_16.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_16.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_16-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_16.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_16.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_16-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_16.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_16.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_16-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_16.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_17.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_17.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_17-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_17.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_17.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_17-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_17.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_17.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_17-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_17.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_18.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_18.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_18-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_18.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_18.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_18-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_18.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_18.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_18-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_18.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_19.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_19.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_19-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_19.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_19.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_19-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_19.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_19.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_19-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_19.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19-normalized.nii.gz -rescale 0 200 -double mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-normalized.nii.gz -sub segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19-normalized.nii.gz -sq -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz -kernel 3 -mean segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz -mul -27 -div 10000 -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz mirtk calculate segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz -exp -out segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz mirtk calculate-filtering segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz -kernel 3 -median segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/segmentations-v3/ALBERT_20.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_20.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_20-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/tissues-v3/ALBERT_20.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_20.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_20-n.dof.gz -interp NN mirtk transform-image /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/atlases/ALBERTs/T2/ALBERT_20.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_20.nii.gz -target N4/sub-NYS1553-ses-001.nii.gz -dofin dofs/sub-NYS1553-ses-001-ALBERT_20-n.dof.gz -interp BSpline mirtk normalize N4/sub-NYS1553-ses-001.nii.gz segmentations-data/transformations/T2-sub-NYS1553-ses-001-ALBERT_20.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_20-normalized.nii.gz -piecewise mirtk convert-image segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_20-normalized.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_20-normalized.nii.gz -rescale 0 200 -double mirtk 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segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_14.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_15.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_16.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_17.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_18.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_19.nii.gz segmentations-data/transformations/sub-NYS1553-ses-001-ALBERT_20.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_20.nii.gz 53 1 2 3 4 17 18 19 40 41 42 43 44 45 46 47 48 49 50 85 86 87 5 6 7 8 9 10 11 12 13 14 15 16 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 segmentations-data/labels/seg1/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg2/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg3/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg4/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg17/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg18/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg19/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg40/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg41/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg42/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg43/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg44/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg45/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg46/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg47/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg48/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg49/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg50/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg85/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg86/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg87/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg5/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg6/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg7/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg8/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg9/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg10/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg11/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg12/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg13/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg14/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg15/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg16/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg20/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg21/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg22/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg23/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg24/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg25/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg26/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg27/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg28/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg29/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg30/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg31/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg32/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg33/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg34/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg35/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg36/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg37/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg38/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg39/sub-NYS1553-ses-001.nii.gz mirtk split-labels 20 segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_01.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_02.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_03.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_04.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_05.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_06.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_07.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_08.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_09.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_10.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_11.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_12.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_13.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_14.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_15.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_16.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_17.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_18.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_19.nii.gz segmentations-data/transformations/tissues-sub-NYS1553-ses-001-ALBERT_20.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_01.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_02.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_03.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_04.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_05.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_06.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_07.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_08.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_09.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_10.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_11.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_12.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_13.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_14.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_15.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_16.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_17.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_18.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_19.nii.gz segmentations-data/atlas-weights/sub-NYS1553-ses-001-ALBERT_20.nii.gz 6 1 2 3 4 5 6 segmentations-data/labels/csf/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/gm/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/wm/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/outlier/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/hwm/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/lwm/sub-NYS1553-ses-001.nii.gz mirtk calculate-gradients N4/sub-NYS1553-ses-001.nii.gz segmentations-data/MADs/sub-NYS1553-ses-001-grad.nii.gz 0 mirtk calculate-filtering segmentations-data/MADs/sub-NYS1553-ses-001-grad.nii.gz -kernel 5 -median segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz mirtk calculate segmentations-data/MADs/sub-NYS1553-ses-001-grad.nii.gz -sub segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -abs -out segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz mirtk calculate-filtering segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -kernel 5 -median segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz mirtk calculate segmentations-data/MADs/sub-NYS1553-ses-001-grad.nii.gz -div-with-zero segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -div 1.4826 -sq -mul 0.5 -add 1 -log -out segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz mirtk calculate N4/sub-NYS1553-ses-001.nii.gz -div-with-zero N4/sub-NYS1553-ses-001.nii.gz -mul segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -add 1 -out segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz mirtk calculate segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -mul 0 -add 1 -div-with-zero segmentations-data/MADs/sub-NYS1553-ses-001-cur.nii.gz -out segmentations-data/MADs/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg1/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg2/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg3/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg4/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg17/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg18/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg19/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg40/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg41/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg42/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg43/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg44/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg45/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg46/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg47/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg48/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg49/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg50/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg85/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg86/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg87/sub-NYS1553-ses-001.nii.gz -div 100 -mul segmentations-data/MADs/sub-NYS1553-ses-001.nii.gz -out segmentations-data/MADs/sub-NYS1553-ses-001-subspace.nii.gz segmentation.sh sub-NYS1553-ses-001 mirtk calculate segmentations-data/posteriors/hwm/sub-NYS1553-ses-001.nii.gz -add segmentations-data/posteriors/lwm/sub-NYS1553-ses-001.nii.gz -add segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg1/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg1/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg2/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg2/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg3/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg3/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg4/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg4/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg17/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg17/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg18/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg18/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg19/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg19/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg40/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg40/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg41/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg41/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg42/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg42/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg43/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg43/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg44/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg44/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg45/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg45/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg46/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg46/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg47/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg47/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg48/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg48/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg49/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg49/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg50/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg50/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg85/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg85/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg86/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg86/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/seg87/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/seg87/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/outlier/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/outlier/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/csf/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/csf/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/hwm/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/hwm/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/posteriors/lwm/sub-NYS1553-ses-001.nii.gz -mul 100 -out segmentations-data/posteriors/lwm/sub-NYS1553-ses-001.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-em.nii.gz segmentations/sub-NYS1553-ses-001-em.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/seg-numbers.csv separate-hemispheres.sh sub-NYS1553-ses-001 mirtk em-hard-segmentation 32 segmentations-data/labels/seg5/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg6/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg7/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg8/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg9/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg10/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg11/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg12/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg13/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg14/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg15/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg16/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg20/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg21/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg22/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg23/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg24/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg25/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg26/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg27/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg28/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg29/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg30/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg31/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg32/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg33/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg34/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg35/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg36/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg37/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg38/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg39/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz -mrftimes 1 -posteriors segmentations-data/labels/seg5-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg6-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg7-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg8-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg9-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg10-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg11-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg12-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg13-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg14-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg15-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg16-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg20-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg21-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg22-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg23-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg24-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg25-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg26-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg27-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg28-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg29-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg30-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg31-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg32-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg33-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg34-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg35-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg36-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg37-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg38-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg39-extended/sub-NYS1553-ses-001.nii.gz with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 92.499 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 MRF iteration 1...done mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz 1 1 5 1 2 6 1 3 7 1 4 8 1 5 9 1 6 10 1 7 11 1 8 12 1 9 13 1 10 14 1 11 15 1 12 16 1 13 20 1 14 21 1 15 22 1 16 23 1 17 24 1 18 25 1 19 26 1 20 27 1 21 28 1 22 29 1 23 30 1 24 31 1 25 32 1 26 33 1 27 34 1 28 35 1 29 36 1 30 37 1 31 38 1 32 39 mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz 2000 0 -invert mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-cortical-gm.nii.gz 1000 0 -invert mirtk padding segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz 1 5 51 1 6 52 1 7 53 1 8 54 1 9 55 1 10 56 1 11 57 1 12 58 1 13 59 1 14 60 1 15 61 1 16 62 1 20 63 1 21 64 1 22 65 1 23 66 1 24 67 1 25 68 1 26 69 1 27 70 1 28 71 1 29 72 1 30 73 1 31 74 1 32 75 1 33 76 1 34 77 1 35 78 1 36 79 1 37 80 1 38 81 1 39 82 mirtk padding segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001_all_labels_ini-sephemi.nii.gz 2 1000 2000 0 mirtk calculate segmentations/sub-NYS1553-ses-001_all_labels_ini-sephemi.nii.gz -add segmentations/sub-NYS1553-ses-001-cortical-gm.nii.gz -add segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz -out segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_labels-sephemi.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/all-labels-to-labels.csv mirtk padding segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels-sephemi.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/all-labels-to-tissue-labels.csv mirtk calculate segmentations/sub-NYS1553-ses-001_labels-sephemi.nii.gz -mul 0 -out segmentations/sub-NYS1553-ses-001-empty.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-empty.nii.gz segmentations/sub-NYS1553-ses-001_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz 24 1 3 5 7 9 11 13 15 17 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 1 mirtk padding segmentations/sub-NYS1553-ses-001-empty.nii.gz segmentations/sub-NYS1553-ses-001_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz 24 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 50 1 mirtk padding segmentations/sub-NYS1553-ses-001-empty.nii.gz segmentations/sub-NYS1553-ses-001_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001-both-hemisphere.nii.gz 2 19 48 1 mirtk padding segmentations/sub-NYS1553-ses-001-both-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001_all_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001-both-hemisphere.nii.gz 85 1 mirtk calculate-distance-map segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001-L-hemisphere-dmap.nii.gz mirtk calculate-distance-map segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001-R-hemisphere-dmap.nii.gz mirtk smooth-image segmentations/sub-NYS1553-ses-001-L-hemisphere-dmap.nii.gz segmentations/sub-NYS1553-ses-001-L-hemisphere-dmap.nii.gz 1 -float mirtk smooth-image segmentations/sub-NYS1553-ses-001-R-hemisphere-dmap.nii.gz segmentations/sub-NYS1553-ses-001-R-hemisphere-dmap.nii.gz 1 -float mirtk calculate segmentations/sub-NYS1553-ses-001-R-hemisphere-dmap.nii.gz -sub segmentations/sub-NYS1553-ses-001-L-hemisphere-dmap.nii.gz -mask-below 0 -inside 1 -outside 0 -out segmentations/sub-NYS1553-ses-001-hemisphere-cut.nii.gz mirtk calculate segmentations/sub-NYS1553-ses-001-hemisphere-cut.nii.gz -mul segmentations/sub-NYS1553-ses-001-both-hemisphere.nii.gz -add segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz -out segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz mirtk calculate segmentations/sub-NYS1553-ses-001-hemisphere-cut.nii.gz -sub 1 -mul -1 -mul segmentations/sub-NYS1553-ses-001-both-hemisphere.nii.gz -add segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz -out segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_L_white_init.nii.gz 5 1 2 4 6 8 0 mirtk extract-connected-components segmentations/sub-NYS1553-ses-001_L_white_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_L_white_init-lccs.nii.gz -all -output-component-labels -connectivity 6 mirtk padding segmentations/sub-NYS1553-ses-001_L_white_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_L_white_init-lccs.nii.gz segmentations/sub-NYS1553-ses-001_L_white_unfilled.nii.gz 1 1 0 -invert mirtk fill-holes segmentations/sub-NYS1553-ses-001_L_white_unfilled.nii.gz segmentations/sub-NYS1553-ses-001_L_white.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-L-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_L_pial_init.nii.gz 4 1 4 6 8 0 mirtk extract-connected-components segmentations/sub-NYS1553-ses-001_L_pial_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_L_pial_init-lccs.nii.gz -all -output-component-labels -connectivity 6 mirtk padding segmentations/sub-NYS1553-ses-001_L_pial_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_L_pial_init-lccs.nii.gz segmentations/sub-NYS1553-ses-001_L_pial_unfilled.nii.gz 1 1 0 -invert mirtk fill-holes segmentations/sub-NYS1553-ses-001_L_pial_unfilled.nii.gz segmentations/sub-NYS1553-ses-001_L_pial.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_R_white_init.nii.gz 5 1 2 4 6 8 0 mirtk extract-connected-components segmentations/sub-NYS1553-ses-001_R_white_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_R_white_init-lccs.nii.gz -all -output-component-labels -connectivity 6 mirtk padding segmentations/sub-NYS1553-ses-001_R_white_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_R_white_init-lccs.nii.gz segmentations/sub-NYS1553-ses-001_R_white_unfilled.nii.gz 1 1 0 -invert mirtk fill-holes segmentations/sub-NYS1553-ses-001_R_white_unfilled.nii.gz segmentations/sub-NYS1553-ses-001_R_white.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001-R-hemisphere.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels-sephemi.nii.gz segmentations/sub-NYS1553-ses-001_R_pial_init.nii.gz 4 1 4 6 8 0 mirtk extract-connected-components segmentations/sub-NYS1553-ses-001_R_pial_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_R_pial_init-lccs.nii.gz -all -output-component-labels -connectivity 6 mirtk padding segmentations/sub-NYS1553-ses-001_R_pial_init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001_R_pial_init-lccs.nii.gz segmentations/sub-NYS1553-ses-001_R_pial_unfilled.nii.gz 1 1 0 -invert mirtk fill-holes segmentations/sub-NYS1553-ses-001_R_pial_unfilled.nii.gz segmentations/sub-NYS1553-ses-001_R_pial.nii.gz correct-segmentation.sh sub-NYS1553-ses-001 mirtk padding segmentations/sub-NYS1553-ses-001-em.nii.gz segmentations/sub-NYS1553-ses-001-em.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-hwm-init.nii.gz 26 0 -invert mirtk padding segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-ven-init.nii.gz 2 49 50 0 -invert 2 49 50 1 mirtk extract-connected-components segmentations-data/corrections/sub-NYS1553-ses-001-ven-init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-ven-init-lccs.nii.gz -all -output-component-labels -connectivity 6 mirtk padding segmentations-data/corrections/sub-NYS1553-ses-001-ven-init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-ven-init-lccs.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-ven.nii.gz 1 1 0 -invert mirtk calculate segmentations-data/corrections/sub-NYS1553-ses-001-ven-init.nii.gz -sub segmentations-data/corrections/sub-NYS1553-ses-001-ven.nii.gz -out segmentations-data/corrections/sub-NYS1553-ses-001-ven-diff.nii.gz mirtk fill-holes-nn-based segmentations-data/corrections/sub-NYS1553-ses-001-hwm-init.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-ven-diff.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-hwm-fillh.nii.gz mirtk calculate segmentations-data/corrections/sub-NYS1553-ses-001-ven-diff.nii.gz -mul segmentations-data/corrections/sub-NYS1553-ses-001-hwm-fillh.nii.gz -out segmentations-data/corrections/sub-NYS1553-ses-001-ventohwm.nii.gz mirtk calculate segmentations/sub-NYS1553-ses-001-initial.nii.gz -mul 0 -out segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz mirtk calculate segmentations/sub-NYS1553-ses-001_L_white.nii.gz -mul segmentations/sub-NYS1553-ses-001-initial.nii.gz -out segmentations-data/corrections/sub-NYS1553-ses-001-gmmask.nii.gz mirtk padding segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmmask.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz 1000 1 mirtk calculate segmentations/sub-NYS1553-ses-001_R_white.nii.gz -mul segmentations/sub-NYS1553-ses-001-initial.nii.gz -out segmentations-data/corrections/sub-NYS1553-ses-001-gmmask.nii.gz mirtk padding segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmmask.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz 1000 1 mirtk change-label segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz 22 segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz 2000 segmentations-data/posteriors/seg1/sub-NYS1553-ses-001.nii.gz 1 segmentations-data/posteriors/seg2/sub-NYS1553-ses-001.nii.gz 2 segmentations-data/posteriors/seg3/sub-NYS1553-ses-001.nii.gz 3 segmentations-data/posteriors/seg4/sub-NYS1553-ses-001.nii.gz 4 segmentations-data/posteriors/seg17/sub-NYS1553-ses-001.nii.gz 17 segmentations-data/posteriors/seg18/sub-NYS1553-ses-001.nii.gz 18 segmentations-data/posteriors/seg19/sub-NYS1553-ses-001.nii.gz 19 segmentations-data/posteriors/seg40/sub-NYS1553-ses-001.nii.gz 40 segmentations-data/posteriors/seg41/sub-NYS1553-ses-001.nii.gz 41 segmentations-data/posteriors/seg42/sub-NYS1553-ses-001.nii.gz 42 segmentations-data/posteriors/seg43/sub-NYS1553-ses-001.nii.gz 43 segmentations-data/posteriors/seg44/sub-NYS1553-ses-001.nii.gz 44 segmentations-data/posteriors/seg45/sub-NYS1553-ses-001.nii.gz 45 segmentations-data/posteriors/seg46/sub-NYS1553-ses-001.nii.gz 46 segmentations-data/posteriors/seg47/sub-NYS1553-ses-001.nii.gz 47 segmentations-data/posteriors/seg48/sub-NYS1553-ses-001.nii.gz 48 segmentations-data/posteriors/seg49/sub-NYS1553-ses-001.nii.gz 49 segmentations-data/posteriors/seg50/sub-NYS1553-ses-001.nii.gz 50 segmentations-data/posteriors/seg85/sub-NYS1553-ses-001.nii.gz 85 segmentations-data/posteriors/seg86/sub-NYS1553-ses-001.nii.gz 86 segmentations-data/posteriors/seg87/sub-NYS1553-ses-001.nii.gz 87 segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg1/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg2/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg3/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg4/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg17/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg18/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg19/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg40/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg41/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg42/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg43/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg44/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg45/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg46/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg47/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg48/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg49/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg50/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg85/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg86/sub-NYS1553-ses-001.nii.gz segmentations-data/posteriors/seg87/sub-NYS1553-ses-001.nii.gz mirtk padding segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz segmentations-data/corrections/sub-NYS1553-ses-001-gmtochange.nii.gz segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz 1 0 postprocess.sh sub-NYS1553-ses-001 mirtk em-hard-segmentation 32 segmentations-data/labels/seg5/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg6/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg7/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg8/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg9/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg10/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg11/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg12/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg13/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg14/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg15/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg16/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg20/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg21/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg22/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg23/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg24/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg25/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg26/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg27/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg28/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg29/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg30/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg31/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg32/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg33/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg34/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg35/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg36/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg37/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg38/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg39/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz -mrftimes 1 -posteriors segmentations-data/labels/seg5-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg6-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg7-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg8-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg9-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg10-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg11-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg12-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg13-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg14-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg15-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg16-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg20-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg21-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg22-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg23-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg24-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg25-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg26-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg27-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg28-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg29-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg30-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg31-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg32-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg33-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg34-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg35-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg36-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg37-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg38-extended/sub-NYS1553-ses-001.nii.gz segmentations-data/labels/seg39-extended/sub-NYS1553-ses-001.nii.gz with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 92.499 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 with range: 0 - 100 MRF iteration 1...done mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz 1 1 5 1 2 6 1 3 7 1 4 8 1 5 9 1 6 10 1 7 11 1 8 12 1 9 13 1 10 14 1 11 15 1 12 16 1 13 20 1 14 21 1 15 22 1 16 23 1 17 24 1 18 25 1 19 26 1 20 27 1 21 28 1 22 29 1 23 30 1 24 31 1 25 32 1 26 33 1 27 34 1 28 35 1 29 36 1 30 37 1 31 38 1 32 39 mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz 2000 0 -invert mirtk padding segmentations-data/cortical/sub-NYS1553-ses-001.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-cortical-gm.nii.gz 1000 0 -invert mirtk padding segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz 1 5 51 1 6 52 1 7 53 1 8 54 1 9 55 1 10 56 1 11 57 1 12 58 1 13 59 1 14 60 1 15 61 1 16 62 1 20 63 1 21 64 1 22 65 1 23 66 1 24 67 1 25 68 1 26 69 1 27 70 1 28 71 1 29 72 1 30 73 1 31 74 1 32 75 1 33 76 1 34 77 1 35 78 1 36 79 1 37 80 1 38 81 1 39 82 mirtk padding segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001-initial.nii.gz segmentations/sub-NYS1553-ses-001_all_labels_ini.nii.gz 2 1000 2000 0 mirtk calculate segmentations/sub-NYS1553-ses-001_all_labels_ini.nii.gz -add segmentations/sub-NYS1553-ses-001-cortical-gm.nii.gz -add segmentations/sub-NYS1553-ses-001-cortical-wm.nii.gz -out segmentations/sub-NYS1553-ses-001_all_labels.nii.gz mirtk padding segmentations/sub-NYS1553-ses-001_all_labels.nii.gz segmentations/sub-NYS1553-ses-001_all_labels.nii.gz segmentations/sub-NYS1553-ses-001_labels.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/all-labels-to-labels.csv mirtk padding segmentations/sub-NYS1553-ses-001_all_labels.nii.gz segmentations/sub-NYS1553-ses-001_all_labels.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels.nii.gz /usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/parameters/all-labels-to-tissue-labels.csv postprocess-pmaps.sh sub-NYS1553-ses-001 mirtk calculate segmentations-data/labels/seg5-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg6-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg7-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg8-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg9-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg10-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg11-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg12-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg13-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg14-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg15-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg16-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg20-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg21-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg22-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg23-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg24-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg25-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg26-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg27-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg28-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg29-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg30-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg31-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg32-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg33-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg34-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg35-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg36-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg37-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg38-extended/sub-NYS1553-ses-001.nii.gz -add segmentations-data/labels/seg39-extended/sub-NYS1553-ses-001.nii.gz -out segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz mirtk calculate segmentations-data/labels/seg5-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg5/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg5-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg51/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg6-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg6/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg6-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg52/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg7-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg7/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg7-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg53/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg8-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg8/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg8-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg54/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg9-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg9/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg9-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg55/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg10-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg10/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg10-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg56/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg11-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg11/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg11-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg57/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg12-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg12/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg12-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg58/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg13-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg13/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg13-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg59/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg14-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg14/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg14-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg60/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg15-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg15/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg15-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg61/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg16-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg16/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg16-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg62/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg20-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg20/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg20-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg63/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg21-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg21/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg21-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg64/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg22-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg22/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg22-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg65/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg23-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg23/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg23-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg66/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg24-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg24/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg24-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg67/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg25-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg25/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg25-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg68/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg26-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg26/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg26-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg69/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg27-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg27/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg27-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg70/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg28-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg28/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg28-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg71/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg29-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg29/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg29-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg72/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg30-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg30/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg30-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg73/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg31-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg31/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg31-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg74/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg32-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg32/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg32-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg75/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg33-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg33/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg33-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg76/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg34-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg34/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg34-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg77/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg35-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg35/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg35-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg78/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg36-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg36/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg36-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg79/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg37-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg37/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg37-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg80/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg38-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg38/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg38-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg81/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg39-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/gm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg39/sub-NYS1553-ses-001.nii.gz mirtk calculate segmentations-data/labels/seg39-extended/sub-NYS1553-ses-001.nii.gz -div-with-zero segmentations-data/posteriors/temp/sub-NYS1553-ses-001-gmwm.nii.gz -mul segmentations-data/posteriors/wm/sub-NYS1553-ses-001.nii.gz -out posteriors/seg82/sub-NYS1553-ses-001.nii.gz clear-data.sh sub-NYS1553-ses-001 ---------------------------- mirtk padding segmentations/sub-NYS1553-ses-001_tissue_labels.nii.gz segmentations/sub-NYS1553-ses-001_tissue_labels.nii.gz masks/sub-NYS1553-ses-001-labels.nii.gz 2 1 4 0 fslmaths masks/sub-NYS1553-ses-001-labels.nii.gz -bin -dilD -dilD -dilD -ero -ero masks/sub-NYS1553-ses-001-dil.nii.gz wb_command -volume-fill-holes masks/sub-NYS1553-ses-001-dil.nii.gz masks/sub-NYS1553-ses-001.nii.gz