segment-stack

Segment the fetal brain ROI from each stack using a CNN model (MONAIfbs). Check out the original repo for details.

usage: nesvor segment-stack --input-stacks str [str ...]
                            [--stack-masks str [str ...]] [--volume-mask str]
                            [--stacks-intersection]
                            [--background-threshold float]
                            [--otsu-thresholding] --output-stack-masks str
                            [str ...] [--output-json str]
                            [--batch-size-seg int] [--no-augmentation-seg]
                            [--dilation-radius-seg float]
                            [--threshold-small-seg float] [--device int]
                            [--verbose int] [--output-log str] [--seed int]
                            [--debug]

inputs

--input-stacks

Type: str [str ...]

Paths to the input stacks (NIfTI).

input stacks masking

--stack-masks

Type: str [str ...]

Paths to masks of input stacks.

--volume-mask

Type: str

Paths to a 3D mask which will be applied to each input stack.

--stacks-intersection

Only consider the region defined by the intersection of input stacks. Will be ignored if --volume-mask is provided.

--background-threshold

Type: float

Default: 0

pixels with value <= this threshold will be ignored.

--otsu-thresholding

Apply Otsu thresholding to each input stack.

outputs

--output-stack-masks

Type: str [str ...]

Path to the output folder or list of pathes to the output masks

--output-json

Type: str

Path to a json file for saving the inputs and results of the command.

fetal brain masking

--batch-size-seg

Type: int

Default: 16

Batch size for segmentation

--no-augmentation-seg

Disable inference data augmentation in segmentation

--dilation-radius-seg

Type: float

Default: 1.0

Dilation radius for segmentation mask in millimeter.

--threshold-small-seg

Type: float

Default: 0.1

Threshold for removing small segmetation mask (between 0 and 1). A mask will be removed if its area < threshold * max area in the stack.

miscellaneous

--device

Type: int

Default: 0

Id of the device to use. Use GPU if it is nonnegative and use CPU if it is negative.

--verbose

Possible choices: 0, 1, 2

Default: 1

Level of verbosity: (0: warning/error, 1: info, 2: debug)

--output-log

Type: str

Path to the output log file

--seed

Type: int

Random seed

--debug

Debug mode.