sample-volume

Sample a volume from a trained NeSVoR model.

usage: nesvor sample-volume --input-model str --output-volume str
                            [--output-json str] [--output-resolution float]
                            [--output-intensity-mean float]
                            [--inference-batch-size int]
                            [--n-inference-samples int]
                            [--output-psf-factor float]
                            [--sample-orientation str] [--sample-mask str]
                            [--device int] [--verbose int] [--output-log str]
                            [--seed int] [--debug]

inputs

--input-model

Type: str

Path to the trained NeSVoR model.

outputs

--output-volume

Type: str

Paths to the reconstructed volume

--output-json

Type: str

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

outputs sampling

--output-resolution

Type: float

Default: 0.8

Isotropic resolution of the reconstructed volume

--output-intensity-mean

Type: float

Default: 700.0

mean intensity of the output volume

--inference-batch-size

Type: int

Default: 32768

batch size for inference

--n-inference-samples

Type: int

Default: 512

number of sample for PSF during inference

--output-psf-factor

Type: float

Default: 1.0

Determind the psf for generating output volume: FWHM = output-resolution * output-psf-factor

--sample-orientation

Type: str

Path to a nii file. The sampled volume will be reoriented according to the transformatio in this file.

--sample-mask

Type: str

3D Mask for sampling INR. If not provided, will use a mask esitmated from the input data.

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.