correct-bias-field

Perform bias field correction for each input stack with the N4 algorithm.

usage: nesvor correct-bias-field --input-stacks str [str ...]
                                 [--stack-masks str [str ...]]
                                 [--volume-mask str] [--stacks-intersection]
                                 [--background-threshold float]
                                 [--otsu-thresholding]
                                 --output-corrected-stacks str [str ...]
                                 [--output-json str] [--n-proc-n4 int]
                                 [--shrink-factor-n4 int] [--tol-n4 float]
                                 [--spline-order-n4 int] [--noise-n4 float]
                                 [--n-iter-n4 int] [--n-levels-n4 int]
                                 [--n-control-points-n4 int] [--n-bins-n4 int]
                                 [--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-corrected-stacks

Type: str [str ...]

Path to the output folder or list of pathes to the output corrected stacks

--output-json

Type: str

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

N4 bias field correction

--n-proc-n4

Type: int

Default: 8

number of workers for the N4 algorithm.

--shrink-factor-n4

Type: int

Default: 2

The shrink factor used to reduce the size and complexity of the image.

--tol-n4

Type: float

Default: 0.001

The convergence threshold in N4.

--spline-order-n4

Type: int

Default: 3

The order of B-spline.

--noise-n4

Type: float

Default: 0.01

The noise estimate defining the Wiener filter.

--n-iter-n4

Type: int

Default: 50

The maximum number of iterations specified at each fitting level.

--n-levels-n4

Type: int

Default: 4

The maximum number of iterations specified at each fitting level.

--n-control-points-n4

Type: int

Default: 4

The control point grid size in each dimension. The B-spline mesh size is equal to the number of control points in that dimension minus the spline order.

--n-bins-n4

Type: int

Default: 200

The number of bins in the log input intensity histogram.

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.