additional files for the dHCP pipeline
Subject:    subjectNN_DTI_0317_MR1-session1 
Directory:  /gpfs/home2/fsavvopo/analysis/dHCP_final/NN_DTI_0317_MR1/workdir/subjectNN_DTI_0317_MR1-session1 
Threads:    1

/usr/src/structural-pipeline/scripts/misc/pipeline.sh subjectNN_DTI_0317_MR1-session1 33 -d /gpfs/home2/fsavvopo/analysis/dHCP_final/NN_DTI_0317_MR1/workdir/subjectNN_DTI_0317_MR1-session1 -t 1
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fslmaths restore/T2/subjectNN_DTI_0317_MR1-session1.nii.gz -thr 0 restore/T2/subjectNN_DTI_0317_MR1-session1.nii.gz
N4 3 -i restore/T2/subjectNN_DTI_0317_MR1-session1.nii.gz -x masks/subjectNN_DTI_0317_MR1-session1-bet.nii.gz -o [restore/T2/subjectNN_DTI_0317_MR1-session1_restore.nii.gz,restore/T2/subjectNN_DTI_0317_MR1-session1_bias.nii.gz] -c [50x50x50,0.001] -s 2 -b [100,3] -t [0.15,0.01,200]
fslmaths restore/T2/subjectNN_DTI_0317_MR1-session1_restore.nii.gz -mul masks/subjectNN_DTI_0317_MR1-session1.nii.gz restore/T2/subjectNN_DTI_0317_MR1-session1_restore_brain.nii.gz
fslmaths restore/T2/subjectNN_DTI_0317_MR1-session1_restore.nii.gz -mul masks/subjectNN_DTI_0317_MR1-session1-bet.nii.gz restore/T2/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz
mirtk transform-image /usr/src/structural-pipeline/parameters/deface/template-33-facemask.nii.gz masks/subjectNN_DTI_0317_MR1-session1_serag_mask.nii.gz -dofin dofs/subjectNN_DTI_0317_MR1-session1-template-33-n.dof.gz -target restore/T2/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz -Sp 1
fslmaths masks/subjectNN_DTI_0317_MR1-session1_serag_mask.nii.gz -add masks/subjectNN_DTI_0317_MR1-session1.nii.gz -bin masks/subjectNN_DTI_0317_MR1-session1_mask_defaced.nii.gz
fslmaths restore/T2/subjectNN_DTI_0317_MR1-session1.nii.gz -mul masks/subjectNN_DTI_0317_MR1-session1_mask_defaced.nii.gz restore/T2/subjectNN_DTI_0317_MR1-session1_defaced.nii.gz
fslmaths restore/T2/subjectNN_DTI_0317_MR1-session1_restore.nii.gz -mul masks/subjectNN_DTI_0317_MR1-session1_mask_defaced.nii.gz restore/T2/subjectNN_DTI_0317_MR1-session1_restore_defaced.nii.gz
mirtk register restore/T2/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-33.nii.gz -dofout dofs/template-33-subjectNN_DTI_0317_MR1-session1-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 1 -v 0
mirtk convert-dof dofs/subjectNN_DTI_0317_MR1-session1-template-33-n.dof.gz dofs/subjectNN_DTI_0317_MR1-session1-template-33-r.dof.gz -input-format mirtk -output-format rigid
mirtk convert-dof dofs/subjectNN_DTI_0317_MR1-session1-template-33-n.dof.gz dofs/subjectNN_DTI_0317_MR1-session1-template-33-a.dof.gz -output-format affine
mirtk compose-dofs dofs/subjectNN_DTI_0317_MR1-session1-template-33-a.dof.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/dofs/33-40-a.dof.gz dofs/subjectNN_DTI_0317_MR1-session1-template-40-i.dof.gz -target restore/T2/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz
mirtk register restore/T2/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/T2/template-40.nii.gz -dofin dofs/subjectNN_DTI_0317_MR1-session1-template-40-i.dof.gz -dofout dofs/subjectNN_DTI_0317_MR1-session1-template-40-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 1 -v 0
rm dofs/subjectNN_DTI_0317_MR1-session1-template-33-a.dof.gz dofs/subjectNN_DTI_0317_MR1-session1-template-40-i.dof.gz
mirtk convert-dof dofs/template-33-subjectNN_DTI_0317_MR1-session1-n.dof.gz dofs/template-33-subjectNN_DTI_0317_MR1-session1-a.dof.gz -output-format affine
mirtk compose-dofs /usr/src/structural-pipeline/parameters/../atlases/non-rigid-v2/dofs/40-33-a.dof.gz dofs/template-33-subjectNN_DTI_0317_MR1-session1-a.dof.gz dofs/template-40-subjectNN_DTI_0317_MR1-session1-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/subjectNN_DTI_0317_MR1-session1_restore_bet.nii.gz -dofin dofs/template-40-subjectNN_DTI_0317_MR1-session1-i.dof.gz -dofout dofs/template-40-subjectNN_DTI_0317_MR1-session1-n.dof.gz -parin /usr/src/structural-pipeline/parameters/ireg.cfg -threads 1 -v 0
rm dofs/template-33-subjectNN_DTI_0317_MR1-session1-a.dof.gz dofs/template-40-subjectNN_DTI_0317_MR1-session1-i.dof.gz