additional files for the dHCP pipeline
Subject:    sub-NYS1553-ses-001 
Directory:  /data/workdir/sub-NYS1553-ses-001 
Threads:    8

/usr/src/structural-pipeline/scripts/misc/pipeline.sh sub-NYS1553-ses-001 43 -d /data/workdir/sub-NYS1553-ses-001 -t 8
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fslmaths restore/T2/sub-NYS1553-ses-001.nii.gz -thr 0 restore/T2/sub-NYS1553-ses-001.nii.gz
N4 3 -i restore/T2/sub-NYS1553-ses-001.nii.gz -x masks/sub-NYS1553-ses-001-bet.nii.gz -o [restore/T2/sub-NYS1553-ses-001_restore.nii.gz,restore/T2/sub-NYS1553-ses-001_bias.nii.gz] -c [50x50x50,0.001] -s 2 -b [100,3] -t [0.15,0.01,200]
fslmaths restore/T2/sub-NYS1553-ses-001_restore.nii.gz -mul masks/sub-NYS1553-ses-001.nii.gz restore/T2/sub-NYS1553-ses-001_restore_brain.nii.gz
fslmaths restore/T2/sub-NYS1553-ses-001_restore.nii.gz -mul masks/sub-NYS1553-ses-001-bet.nii.gz restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz
mirtk transform-image /usr/src/structural-pipeline/parameters/deface/template-43-facemask.nii.gz masks/sub-NYS1553-ses-001_serag_mask.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-43-n.dof.gz -target restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz -Sp 1
fslmaths masks/sub-NYS1553-ses-001_serag_mask.nii.gz -add masks/sub-NYS1553-ses-001.nii.gz -bin masks/sub-NYS1553-ses-001_mask_defaced.nii.gz
fslmaths restore/T2/sub-NYS1553-ses-001.nii.gz -mul masks/sub-NYS1553-ses-001_mask_defaced.nii.gz restore/T2/sub-NYS1553-ses-001_defaced.nii.gz
fslmaths restore/T2/sub-NYS1553-ses-001_restore.nii.gz -mul masks/sub-NYS1553-ses-001_mask_defaced.nii.gz restore/T2/sub-NYS1553-ses-001_restore_defaced.nii.gz
mirtk register restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-43.nii.gz -dofout dofs/template-43-sub-NYS1553-ses-001-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 8 -v 0
mirtk convert-dof dofs/sub-NYS1553-ses-001-template-43-n.dof.gz dofs/sub-NYS1553-ses-001-template-43-r.dof.gz -input-format mirtk -output-format rigid
mirtk convert-dof dofs/sub-NYS1553-ses-001-template-43-n.dof.gz dofs/sub-NYS1553-ses-001-template-43-a.dof.gz -output-format affine
mirtk compose-dofs dofs/sub-NYS1553-ses-001-template-43-a.dof.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/dofs/43-40-a.dof.gz dofs/sub-NYS1553-ses-001-template-40-i.dof.gz -target restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz
mirtk register restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-40.nii.gz -dofin dofs/sub-NYS1553-ses-001-template-40-i.dof.gz -dofout dofs/sub-NYS1553-ses-001-template-40-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 8 -v 0
rm dofs/sub-NYS1553-ses-001-template-43-a.dof.gz dofs/sub-NYS1553-ses-001-template-40-i.dof.gz
mirtk convert-dof dofs/template-43-sub-NYS1553-ses-001-n.dof.gz dofs/template-43-sub-NYS1553-ses-001-a.dof.gz -output-format affine
mirtk compose-dofs /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/dofs/40-43-a.dof.gz dofs/template-43-sub-NYS1553-ses-001-a.dof.gz dofs/template-40-sub-NYS1553-ses-001-i.dof.gz -target /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-40.nii.gz
mirtk register /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-40.nii.gz restore/T2/sub-NYS1553-ses-001_restore_bet.nii.gz -dofin dofs/template-40-sub-NYS1553-ses-001-i.dof.gz -dofout dofs/template-40-sub-NYS1553-ses-001-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 8 -v 0
rm dofs/template-43-sub-NYS1553-ses-001-a.dof.gz dofs/template-40-sub-NYS1553-ses-001-i.dof.gz