# name type default (valid values)/range description group. NB. File should end with newline
device str gpu gpu cpu "Which type of processor to use" general
mode str white black white "Extract black or white tubular structures" general
display bool false "Display results" advanced
centerline-method str gpu test gpu ridge "Centerline extraction method" general
gvf-iterations num 250 0 10000 50 "Number of GVF iterations" gradient-vector-flow
radius-min num 0.5 0.5 50.0 0.5 "Minimum radius of tubular structures" tube-detection-filter
radius-max num 15.0 2.0 300.0 1.0 "Maximum radius of tubular structures" tube-detection-filter
radius-step num 1.0 0.0 5.0 0.5 "Step size of radius" tube-detection-filter
fmax num 0.2 0.01 0.9 0.01 "Maximum gradient length (for contrast invariance)" general
gvf-mu num 0.05 0.0 0.5 0.01 "Mu regularization constant of GVF" gradient-vector-flow
small-blur num 0.0 0.0 5.0 0.5 "Std. Dev. of Gaussian blur for small tubular structures" general
large-blur num 1.0 0.0 15.0 0.5 "Std. Dev. of Gaussian blur for large tubular structures" general
tdf-high num 0.5 0.1 1.0 0.1 "TDF response threshold" centerline-general
min-distance num 5 0 100 1 "Minimum length for accepting centerlines (ridge traversal)" centerline-ridge
m-low num 0.05 0.0 0.2 0.01 "Threshold of vector field magnitude (ridge traversal)" centerline-ridge
tdf-low num 0.5 0.0 1.0 0.1 "TDF response lower threshold (ridge traversal)" centerline-ridge
max-below-tdf-low num 0 0 5 1 "Number of allowed voxels below TDF lower threshold (ridge traversal)" centerline-ridge
min-mean-tdf num 0.5 0.0 1.0 0.01 "Minimum mean TDF response along centerline" centerline-general
min-tree-length num 5 0 1000 5 "Minimum centerline tree length" centerline-general
timing bool false "Timing of application" advanced
cube-size num 4 0 10 1 "Grid size of (parallel centerline extraction)" centerline-gpu
max-distance num 25.0 0.0 50.0 1.0 "Max distance for connecting two centerpoints (parallel centerline extraction)" centerline-gpu
centerpoints-only bool false "Extract centerpoints only (parallel centerline extraction)" centerline-gpu
tdf-only bool false "Generate TDF response only" tube-detection-filter
no-segmentation bool false "Don't perform segmentation" general
centerline-vtk-file str off "Filepath to centerline VTK file (ommit to skip)" storage
sphere-segmentation bool false "Do a simple sphere segmentation" general
minimum str off "Minimum intensity value" general
maximum str off "Maximum intensity value" general
cropping str no no lung threshold "Cropping method" cropping
min-scan-lines-threshold num 10 0 1024 1 "Minimum nr. of scan lines (threshold cropping)" cropping
min-scan-lines-lung num 200 0 1024 1 "Minimum nr. of scan lines (lung cropping)" cropping
cropping-threshold num 0 0 3000 10 "Cropping threshold" cropping
cropping-start-z str end end middle "Where to start cropping in the z direction" cropping
buffers-only bool false "Use OpenCL buffers instead of 3D textures" advanced
storage-dir str off "Directory of where to store results (ommit to skip)" storage
storage-name str unnamed "Storage name" storage
32bit-vectors bool false "Force the use of 32 bit vectors" advanced
16bit-vectors bool true "Force the use of 16 bit vectors" advanced
parameters str none none AAA-Vessels-CT Liver-Vessels-CT Liver-Vessels-MR Lung-Airways-CT Neuro-Vessels-USA Neuro-Vessels-MRA Phantom-Acc-US Synthetic-Vascusynth "Which parameter preset to use" preset
loop-removal bool true "Perform loop removal on centerlines on CPU" advanced
timer-total bool false "Measure the total execution time" advanced
max-edge-distance num 3 2 30 1 "Maxium distance between two vertices in the vtk centerline file. If an edge has a length above it, more vertices and edges will be created in between" centerline-gpu
use-spline-tdf bool false "Use Spline TDF" tube-detection-filter
use-fmg-gvf bool false "Use FMG GVF" gradient-vector-flow
