slicerio 0.1.3

Utilities for 3D Slicer

slicerio

Python utilities for 3D Slicer interoperability.

The package contains utility functions for reading and writing segmentation files. More functions will be added in the future.

Installation

Using pip:

pip install slicerio

Examples

Read segmentation and show some information about segments

import slicerio
import json

segmentation_info = slicerio.read_segmentation_info("Segmentation.seg.nrrd")

number_of_segments = len(segmentation_info["segments"])
print(f"Number of segments: {number_of_segments}")

segment_names = slicerio.segment_names(segmentation_info)
print(f"Segment names: {', '.join(segment_names)}")

segment0 = slicerio.segment_from_name(segmentation_info, segment_names[0])
print("First segment info:\n" + json.dumps(segment0, sort_keys=False, indent=4))

Extract selected segments with chosen label values

import slicerio
import nrrd

input_filename = "path/to/Segmentation.seg.nrrd"
output_filename = "path/to/SegmentationExtracted.seg.nrrd"
segment_names_to_labels = [("ribs", 10), ("right lung", 12), ("left lung", 6)]

voxels, header = nrrd.read(input_filename)
extracted_voxels, extracted_header = slicerio.extract_segments(voxels, header, segmentation_info, segment_names_to_labels)
nrrd.write(output_filename, extracted_voxels, extracted_header)