assess

Assess the quality and motion of each input stack. The output metrics can be used for determining the template stack or removing low-quality data

usage: nesvor assess --input-stacks str [str ...]
                     [--stack-masks str [str ...]] [--volume-mask str]
                     [--stacks-intersection] [--background-threshold float]
                     [--otsu-thresholding] [--output-json str] [--metric str]
                     [--filter-method str] [--cutoff float]
                     [--batch-size-assess int] [--no-augmentation-assess]
                     [--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-json

Type: str

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

stack assessment

--metric

Possible choices: ncc, matrix-rank, volume, iqa2d, iqa3d, none

Default: ncc

Metric for assessing input stacks.

1. ncc (↑): cross correlaiton between adjacent slices;

2. matrix-rank (↓): motion metric based on the rank of the data matrix;

3. volume (↑): volume of the masked ROI;

4. iqa2d (↑): image quality score generated by a 2D CNN (only for fetal brain), the score of a stack is the average score of the images in it;

5. iqa3d (↑): image quality score generated by a 3D CNN (only for fetal brain);

6. none: no metric used for assessment.

Note: (↑) means a stack with a higher score will have a better rank.

--filter-method

Possible choices: top, bottom, threshold, percentage, none

Default: none

Method to remove low-quality stacks.

1. top: keep the top C stacks;

2. bottom: remove the bottom C stacks;

3. threshold: remove a stack if the metric is worse than C;

4. percentatge: remove the bottom (num_stack * C) stacks;

5. none: no filtering.

The value of C is specified by --cutoff.

--cutoff

Type: float

The cutoff value for filtering, i.e., the value C in --filter-method

--batch-size-assess

Type: int

Default: 8

Batch size for IQA network

--no-augmentation-assess

Disable inference data augmentation in IQA network

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.