DOI: 10.5281/zenodo.601461
title: Gold Atlas - Male Pelvis - Gentle Radiotherapy

description: Magnetic resonance images (MRI) (T1w and T2w) with flat table top, and CT images of 19 male patients. The imaging was performed over the pelvic region. In addition there is a CT image that is deformably registered to the MR data. 5 expert observers have independently delineated organs relevant for radiotherapy on all patients. Also included is a consensus delineation of each structure and a STAPLE.

All data is stored in DICOM format.

A publication describing the data set in detail is submitted.

The purpose of the dataset is training or validation of methods for automatic segmentation or conversion from MR to CT.

<strong>Please cite:</strong>

Nyholm, Tufve, Stina Svensson, Sebastian Andersson, Joakim Jonsson, Maja Sohlin, Christian Gustafsson, Elisabeth Kjellén, et al. 2018. “MR and CT Data with Multi Observer Delineations of Organs in the Pelvic Area - Part of the Gold Atlas Project.” <em>Medical Physics</em> 12 (10): 3218–21. doi:10.1002/mp.12748.

 

<strong>ELASTIX parameter files used:</strong>

Registration site 1. 

(FixedInternalImagePixelType "float")

(MovingInternalImagePixelType "float")<br>
(FixedImageDimension 3)<br>
(MovingImageDimension 3)<br>
(UseDirectionCosines "true")

// **************** Main Components **************************<br>
(Registration "MultiMetricMultiResolutionRegistration")<br>
(ResampleInterpolator "FinalBSplineInterpolator")<br>
(Resampler "OpenCLResampler")<br>
(OpenCLResamplerUseOpenCL "true")<br>
(FixedImagePyramid "FixedSmoothingImagePyramid"  "FixedSmoothingImagePyramid" )<br>
(MovingImagePyramid "MovingSmoothingImagePyramid"  "MovingSmoothingImagePyramid" )<br>
(Interpolator "BSplineInterpolator" "BSplineInterpolator" )<br>
(Metric "NormalizedMutualInformation" "AdvancedMeanSquares")<br>
(Metric0Weight 30000)<br>
(Metric1Weight 1)<br>
(Optimizer "AdaptiveStochasticGradientDescent")<br>
(Transform "BSplineTransform")

// ******************** Multiresolution **********************<br>
(NumberOfResolutions 3)<br>
(ImagePyramidSchedule 4.0 4.0 4.0 2.0 2.0 2.0 1.0 1.0 1.0)

// ***************** Transformation **************************<br>
(FinalGridSpacingInPhysicalUnits 60 60 60)<br>
(GridSpacingSchedule 4 2 1)<br>
(AutomaticScalesEstimation "true")<br>
(AutomaticTransformInitialization "false")<br>
(HowToCombineTransforms "Compose")

// ******************* Optimizer ****************************<br>
(MaximumNumberOfIterations 500 500 500)

// ******************* Similarity measure *********************<br>
(NumberOfHistogramBins 64 96 96)<br>
(ErodeMask "false")

// **************** Image sampling **********************<br>
(NumberOfSpatialSamples 3000)<br>
(NewSamplesEveryIteration "true")<br>
(ImageSampler "RandomCoordinate" "RandomCoordinate")<br>
(CheckNumberOfSamples "true")<br>
(RequiredRatioOfValidSamples 0.01)<br>
(UseRandomSampleRegion "true")<br>
(SampleRegionSize 150 150 70) <br>
(MaximumNumberOfSamplingAttempts 100) 

// ************* Interpolation and Resampling ****************<br>
(BSplineInterpolationOrder 2)<br>
(FinalBSplineInterpolationOrder 3)<br>
(DefaultPixelValue -1)<br>
(WriteResultImage "false")<br>
(ResultImagePixelType "short")<br>
(ResultImageFormat "mhd")

 

Registration site 2:

(FixedInternalImagePixelType "float")<br>
(MovingInternalImagePixelType "float")<br>
(FixedImageDimension 3)<br>
(MovingImageDimension 3)<br>
(UseDirectionCosines "true")

// **************** Main Components **************************<br>
(Registration "MultiMetricMultiResolutionRegistration")<br>
(ResampleInterpolator "FinalBSplineInterpolator")<br>
(Resampler "OpenCLResampler")<br>
(OpenCLResamplerUseOpenCL "true")<br>
(FixedImagePyramid "FixedSmoothingImagePyramid"  "FixedSmoothingImagePyramid" )<br>
(MovingImagePyramid "MovingSmoothingImagePyramid"  "MovingSmoothingImagePyramid" )<br>
(Interpolator "BSplineInterpolator" "BSplineInterpolator" )<br>
(Metric "NormalizedMutualInformation" "AdvancedMeanSquares")<br>
(Metric0Weight 15000)<br>
(Metric1Weight 1)<br>
(Optimizer "AdaptiveStochasticGradientDescent")<br>
(Transform "BSplineTransform")

// ******************** Multiresolution **********************<br>
(NumberOfResolutions 3)<br>
(ImagePyramidSchedule 4.0 4.0 4.0 2.0 2.0 2.0 1.0 1.0 1.0)

// ***************** Transformation **************************<br>
(FinalGridSpacingInPhysicalUnits 60 60 60)<br>
(GridSpacingSchedule 4 2 1)<br>
(AutomaticScalesEstimation "true")<br>
(AutomaticTransformInitialization "false")<br>
(HowToCombineTransforms "Compose")

// ******************* Optimizer ****************************<br>
(MaximumNumberOfIterations 500 500 500)

// ******************* Similarity measure *********************<br>
(NumberOfHistogramBins 64 96 96)<br>
(ErodeMask "false")

// **************** Image sampling **********************<br>
(NumberOfSpatialSamples 3000)<br>
(NewSamplesEveryIteration "true")<br>
(ImageSampler "RandomCoordinate" "RandomCoordinate")<br>
(CheckNumberOfSamples "true")<br>
(RequiredRatioOfValidSamples 0.01)<br>
(UseRandomSampleRegion "false")

// ************* Interpolation and Resampling ****************<br>
(BSplineInterpolationOrder 2)<br>
(FinalBSplineInterpolationOrder 3)<br>
(DefaultPixelValue -1)<br>
(WriteResultImage "false")<br>
(ResultImagePixelType "short")<br>
(ResultImageFormat "mhd")

 

Registation site 3:

(FixedInternalImagePixelType "float")<br>
(MovingInternalImagePixelType "float")<br>
(FixedImageDimension 3)<br>
(MovingImageDimension 3)<br>
(UseDirectionCosines "true")

// **************** Main Components **************************<br>
(Registration "MultiMetricMultiResolutionRegistration")<br>
(ResampleInterpolator "FinalBSplineInterpolator")<br>
(Resampler "OpenCLResampler")<br>
(OpenCLResamplerUseOpenCL "true")<br>
(FixedImagePyramid "FixedSmoothingImagePyramid"  "FixedSmoothingImagePyramid" )<br>
(MovingImagePyramid "MovingSmoothingImagePyramid"  "MovingSmoothingImagePyramid" )<br>
(Interpolator "BSplineInterpolator" "BSplineInterpolator" )<br>
(Metric "NormalizedMutualInformation" "AdvancedMeanSquares")<br>
(Metric0Weight 50000)<br>
(Metric1Weight 1)<br>
(Optimizer "AdaptiveStochasticGradientDescent")<br>
(Transform "BSplineTransform")

// ******************** Multiresolution **********************<br>
(NumberOfResolutions 3)<br>
(ImagePyramidSchedule 4.0 4.0 4.0 2.0 2.0 2.0 1.0 1.0 1.0)

// ***************** Transformation **************************<br>
(FinalGridSpacingInPhysicalUnits 60 60 60)<br>
(GridSpacingSchedule 4 2 1)<br>
(AutomaticScalesEstimation "true")<br>
(AutomaticTransformInitialization "false")<br>
(HowToCombineTransforms "Compose")

// ******************* Optimizer ****************************<br>
(MaximumNumberOfIterations 50 50 100)

// ******************* Similarity measure *********************<br>
(NumberOfHistogramBins 64 96 96)<br>
(ErodeMask "false")

// **************** Image sampling **********************<br>
(NumberOfSpatialSamples 3000)<br>
(NewSamplesEveryIteration "true")<br>
(ImageSampler "RandomCoordinate" "RandomCoordinate")<br>
(CheckNumberOfSamples "true")<br>
(RequiredRatioOfValidSamples 0.01)<br>
(UseRandomSampleRegion "true")<br>
(SampleRegionSize 150 150 70) <br>
(MaximumNumberOfSamplingAttempts 100) 

// ************* Interpolation and Resampling ****************<br>
(BSplineInterpolationOrder 2)<br>
(FinalBSplineInterpolationOrder 3)<br>
(DefaultPixelValue -1)<br>
(WriteResultImage "false")<br>
(ResultImagePixelType "short")<br>
(ResultImageFormat "mhd")