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recon-neonatal-cortex.cfg
executable file
·93 lines (79 loc) · 3.77 KB
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recon-neonatal-cortex.cfg
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[recon-neonatal-cortex]
white_matter_labels = 161,160
gray_matter_labels = 1,16
#deep_gray_matter_labels = 85
corpus_callosum_labels = 48
brainstem_labels = 19
cerebellum_labels = 18
right_hemisphere_labels = 1,161
left_hemisphere_labels = 16,160
subcortex_closing = 5
brainstem_closing = 5
cerebellum_closing = 5
temp = %(work_dir)s/cortex-recon/%(subject_id)s-%(session_id)s
prefix = %(temp)/%(subject_id)s-%(session_id)s
temp_dir = %(temp)s
input_t1w_image = %(work_dir)s/restore/T1/%(subject_id)s-%(session_id)s_restore.nii.gz
input_t2w_image = %(work_dir)s/restore/T2/%(subject_id)s-%(session_id)s_restore.nii.gz
input_brain_mask = %(work_dir)s/masks/%(subject_id)s-%(session_id)s.nii.gz
input_labels_image = %(work_dir)s/segmentations/%(subject_id)s-%(session_id)s_all_labels.nii.gz
input_tissues_image = # only labels_image required / used
t1w_image = %(temp_dir)s/t1w-image.nii.gz
t2w_image = %(temp_dir)s/t2w-image.nii.gz
brain_mask = %(temp_dir)s/brain-mask.nii.gz
white_matter_mask = %(temp_dir)s/white-matter-mask.nii.gz
gray_matter_mask = %(temp_dir)s/grey-matter-mask.nii.gz
corpus_callosum_mask = %(temp_dir)s/corpus-callosum-mask.nii.gz
deep_gray_matter_mask = %(temp_dir)s/deep-grey-matter-mask.nii.gz
#ventricles_mask = %(temp_dir)s/ventricles-mask.nii.gz
#ventricles_dmap = %(temp_dir)s/ventricles-dmap.nii.gz
regions_mask = %(temp_dir)s/region-labels.nii.gz
cortical_hull_dmap = %(temp_dir)s/cortical-hull-dmap.nii.gz
# brain_mesh = %(temp_dir)s/brain.vtp
# bs_cb_mesh = %(temp_dir)s/brainstem+cerebellum.vtp
internal_mesh = %(temp_dir)s/internal.vtp
cerebrum_mesh = %(temp_dir)s/cerebrum.vtp
right_cerebrum_mesh = %(temp_dir)s/cerebrum-rh.vtp
left_cerebrum_mesh = %(temp_dir)s/cerebrum-lh.vtp
white_mesh = %(temp_dir)s/white.vtp
pial_mesh = %(temp_dir)s/pial.vtp
right_white_mesh = %(prefix)s.R.white.native.surf.vtk
left_white_mesh = %(prefix)s.L.white.native.surf.vtk
right_pial_mesh = %(prefix)s.R.pial.native.surf.vtk
left_pial_mesh = %(prefix)s.L.pial.native.surf.vtk
## -----------------------------------------------------------------------------
## Parameters of deformable model used to reconstruct WM/cGM surface
##
## Parameter names can use either underscores (_) or dashes (-) as word separators.
## Any underscore is replaced by a dash, and a dash is prepended to the name of
## the parameter. The resulting option string is used to set the value when calling
## the "mirtk deform-mesh" binary to reconstruct the surface.
##
## For example, the following specification in this file:
## gauss_curvature_minimum = .1
## min-active = [5%%, 1%%]
## translates to the following deform-mesh command arguments:
## -gauss-curvature-minimum .1
## -min-active 5% 1%
[recon-neonatal-cortex white_model]
gauss_curvature = 0
min-width = .1
fast-collision-test = False
## -----------------------------------------------------------------------------
## Parameters of deformable model used to reconstruct cGM/CSF (pial) surface
##
## Parameter names can use either underscores (_) or dashes (-) as word separators.
## Any underscore is replaced by a dash, and a dash is prepended to the name of
## the parameter. The resulting option string is used to set the value when calling
## the "mirtk deform-mesh" binary to reconstruct the surface.
##
## For example, the following specification in this file:
## gauss_curvature_minimum = .1
## min-active = [5%%, 1%%]
## translates to the following deform-mesh command arguments:
## -gauss-curvature-minimum .1
## -min-active 5% 1%
[recon-neonatal-cortex pial_model]
gauss_curvature = 0
min-width = .1
fast-collision-test = False