lassoan

# Load dry bone CT of skull into the scene and run this script to automatically segment endocranium

masterVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
smoothingKernelSizeMm = 3.0  # this is used for closing small holes in the se

# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(masterVolumeNode.GetImageData())
thresholdCalculator.SetMethodToOtsu()

lassoan

# The module is now moved to SlicerSandbox extension:
#
#   https://github.com/PerkLab/SlicerSandbox/tree/master/SegmentCrossSectionArea
#

lassoan

# This example script demonstrates how a grow-cut
# operation can be performed without graphical user interface.

# The first half of the script downloads input data and creates seed segments.
# The second half of the script converts segments to merged labelmap (that's the required
# input format for grow-cut filter), computes the complete segmentation, and writes
# results into new segments.

# Generate input data
################################################

lassoan

import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRHead()

# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment("skin")

lassoan

# This gist contained a script that automatically removes table from a CT volume.

# The code was improved and turned into a Slicer module, available in the Sandbox extension:
# https://github.com/PerkLab/SlicerSandbox#remove-ct-table
#
# Source code:
# https://github.com/PerkLab/SlicerSandbox/blob/master/RemoveCtTable/RemoveCtTable.py#L251

lassoan

# Load/generate input data
################################################

# Load master volume
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()

# Define boundary points
import numpy as np

lassoan

#
#
#
#
#
#  This example has been completely reworked and converted to a module, now available at:
#
#
#      https://github.com/lassoan/SlicerLineProfile/blob/master/LineProfile/LineProfile.py
#

lassoan

# Convert volume nodes of 3D Slicer to/from xarray and read/write into zarr format

def xarrayFromVolume(volumeNode) -> "xr.DataArray":
    """Convert an volume node to an xarray.DataArray.
    Origin and spacing metadata is preserved in the xarray's coords. The
    Direction is set in the `direction` attribute.
    Dims are labeled as `x`, `y`, `z`, `t`, and `c`.
    This interface is and behavior is experimental and is subject to possible
    future changes."""
    import xarray as xr

lassoan

# This script can be used with this example scene:
# https://github.com/lassoan/PublicTestingData/releases/download/data/ColoredVolumeRenderingScene.mrb

volumeNode = getNode('Panoramix-cropped')
segmentationNode = getNode('Panoramix-cropped segmentation')
boostSegmentOpacity = False  # Increase voxel value inside segments to allow making them them more opaque

volumesLogic = slicer.modules.volumes.logic()

segmentIds = vtk.vtkStringArray()

lassoan

The example was moved to Sandbox extension so that users can more easily install it:

https://github.com/PerkLab/SlicerSandbox/blob/master/LoadRemoteFile/LoadRemoteFile.py

More information: https://github.com/PerkLab/SlicerSandbox/blob/master/README.md#loadremotefile