Command-Line Interface

The neuroslice command provides a simple interface for brain tumor segmentation from the terminal.

Basic Syntax

neuroslice INPUT OUTPUT [OPTIONS]

Required Arguments:

  • INPUT - Path to input FLAIR NIfTI file (.nii or .nii.gz)

  • OUTPUT - Path to output mask NIfTI file

Optional Arguments:

  • --axis - Slice direction (default: 1)

  • --mode - Processing mode (default: union)

  • --verbose - Show detailed progress

Simple Examples

Process with default settings:

neuroslice FLAIR.nii.gz tumor_mask.nii.gz

Slice Direction Options

Use --axis to specify the slice orientation:

  • axis=0: Sagittal (Left-Right)

  • axis=1: Coronal (Front-Back), default

  • axis=2: Axial (Top-Bottom)

neuroslice input.nii.gz output.nii.gz --axis 0

More than one axis can be specified by providing a comma-separated list:

neuroslice input.nii.gz output.nii.gz --axis 0,1,2

Processing Modes

Union mode (default) creates a mask with only the detected tumor regions:

neuroslice input.nii.gz output.nii.gz --mode union

Cuboid mode creates a bounding box around all detections (better for downstream processing as it provides a convex region):

neuroslice input.nii.gz output.nii.gz --mode cuboid

Complete Example

Process with all options specified:

neuroslice brain_scan.nii.gz result_mask.nii.gz --axis 2 --mode cuboid --verbose

Note

  • Try different orientations if results are suboptimal

  • Use --verbose during initial testing

  • Consider using cuboid mode for downstream processing

See Also