register

Perform inital (rigid) motion correction using SVoRT (only for fetal brain) or stack-to-stack registration.

usage: nesvor register --input-stacks str [str ...]
                       [--thicknesses float [float ...]]
                       [--stack-masks str [str ...]] [--volume-mask str]
                       [--stacks-intersection] [--background-threshold float]
                       [--otsu-thresholding] --output-slices str
                       [--output-json str] [--registration str]
                       [--svort-version str] [--scanner-space] [--device int]
                       [--verbose int] [--output-log str] [--seed int]
                       [--debug]

inputs

--input-stacks

Type: str [str ...]

Paths to the input stacks (NIfTI).

--thicknesses

Type: float [float ...]

Slice thickness of each input stack. If not provided, use the slice gap of the input stack. If only a single number is provided, Assume all input stacks have the same thickness.

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-slices

Type: str

Folder to save the motion corrected slices

--output-json

Type: str

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

rigid registration

--registration

Possible choices: svort, svort-only, svort-stack, stack, none

Default: svort

The type of registration method applied before reconstruction.

1. svort: try SVoRT and stack-to-stack registration and choose the one with better NCC;

2. svort-only: only apply the SVoRT model;

3. svort-stack: only apply the stack transformations of SVoRT;

4. stack: stack-to-stack rigid registration;

5. none: no rigid registration.

Note: The SVoRT model can be only applied to fetal brain data.

--svort-version

Possible choices: v1, v2

Default: v2

Version of SVoRT model

--scanner-space

Perform registration in the scanner space. Default: register the data to the atlas space when svort or svort-stack are used.

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.