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‎README.md‎

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**Cochlea Image Analysis**
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# Cochlea Image Analysis
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<img src="https://github.com/MedicalImageAnalysisTutorials/SlicerCochlea/blob/master/Cochlea.png" width="400" height="400">
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This is a [3D Slicer](https://gaithub.com/Slicer/Slicer) plugin that uses [elastix toolbox](https://github.com/SuperElastix/elastix) for Multi-modal cochlea Images registration, segmentation and analysis. More information can be found [here](https://mtixnat.uni-koblenz.de). The elastix parameters file can be found [here](http://elastix.bigr.nl/wiki/index.php/Par0053)
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This is a [3D Slicer](https://gaithub.com/Slicer/Slicer) plugin that uses [elastix toolbox](https://github.com/SuperElastix/elastix) for Multi-modal cochlea Images registration, segmentation and analysis. The elastix parameters file can be found [here](https://github.com/MedicalImageAnalysisTutorials/SlicerCochlea/tree/master/docs/elastixPars)
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# Tested on
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* Slicer 5.0.3 [for windows](https://slicer-packages.kitware.com/api/v1/file/62d5d2ebe911182f1dc285b2/download) and [for linux](https://slicer-packages.kitware.com/api/v1/file/62cc52d2aa08d161a31c1af2/download). Tested on Windows 10 and Ubuntu 20.04
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* Slicer 4.10.2 [for windows](https://slicer-packages.kitware.com/api/v1/file/60add732ae4540bf6a89c029/download) and [for linux](https://slicer-packages.kitware.com/api/v1/file/60add73aae4540bf6a89c03b/download). Tested on Windows 10 and Ubuntu 18.04
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**Tested on:**
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Slicer 4.10.2 [for windows](https://slicer-packages.kitware.com/api/v1/file/60add732ae4540bf6a89c029/download) and [for linux](https://slicer-packages.kitware.com/api/v1/file/60add73aae4540bf6a89c03b/download). Tested on Windows 10 and Ubuntu 18.04
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This project contains two modules:
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Notice: one can modify the optimiser in elastix parameters to get new results.
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# How to use:
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* In case you are new to 3D Slicer check my [Slicer tutorials](https://www.youtube.com/playlist?list=PLW9iOMxMvikpyCUMmuqiloNp7rpaUl2M1) (notice that there maybe small difference between different versions):
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- [3D Slicer installation](https://www.youtube.com/watch?v=7XHhgpk0m78&list=PLW9iOMxMvikpyCUMmuqiloNp7rpaUl2M1&index=3).
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- [3D Slicer introduction](https://www.youtube.com/watch?v=mmf5eb0WrR8&list=PLW9iOMxMvikpyCUMmuqiloNp7rpaUl2M1&index=4).
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* See the [documentation](https://medicalimageanalysistutorials.github.io/SlicerCochlea/)
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* See the video tutorials for [cochlea registration and fusion](https://www.youtube.com/watch?v=JfEaPO3N47U&t=4s) and [cochlea segmentation and analysis](https://www.youtube.com/watch?v=A_mTcT3eT_c&t=1s)
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# Publications:
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Please cite our papers:
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* Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Rania Helal, Friedrich Lisseck and Roland Jacob, (2018), Automatic Cochlear Length and Volume Size Estimation, Accepted in: First International Workshop on Context-Aware Operating Theater OR 2, MICCAI 2018, Granada Spain.[link](https://or20.univ-rennes1.fr/sites/or20.univ-rennes1.fr/files/asset/document/aldhamarietal2018_0.pdf)
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* Al-Dhamari I, Helal R, Morozova O, Abdelaziz T, Jacob R, et al. (2022) Automatic intra-subject registration and fusion of multimodal cochlea 3D clinical images. PLOS ONE 17(3): e0264449. https://doi.org/10.1371/journal.pone.0264449. [Link](https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264449&type=printable)
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* Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Roland Jacob, (2018), Automatic Cochlea Multi-modal Images Segmentation Using Adaptive Stochastic Gradient Descent. In: CI2018 DC Emerging Issues in Cochlear Implantation, Washington DC, USA.
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* Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Friedrich Lisseck and Roland Jacob, (2017): ACIR: automatic cochlea image registration. In: Proceedings SPIE Medical Imaging 2017: Image Processing;. SPIE. Bd. 10133. S. 10133p1-10133p5. [link](http://spie.org/Publications/Proceedings/Paper/10.1117/12.2254396)
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Please share your cochlea dataset with us.
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Your contribution is welcome!
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# Updates
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Updtaed on 6 August 2022
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Updtae : 6/12/2018
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* Links are updated
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* Master branch is now compitable with Slicer 5
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* Tested on Slicer 5.0.3 on Ubuntu 20.04 and Windows 10
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- Logic and testing classes are added. Some useful functions can be called from external modules. User can test the module using Reload and test button.
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- Runtime libraries are included.
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- Suppport DICOM and other formats.
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- Support filenames with spaces.
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# Notes:
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Tested on Slicer 4.10, Ubuntu 18.04 and Windows 10
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* For general 3D Slicer questions, please use Slicer [forum](https://discourse.slicer.org), many experts will be able to help you there.
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* For Slicer cochlea related questions, comemnts, or feedback, please use github [discussion](https://github.com/MedicalImageAnalysisTutorials/SlicerCochlea/discussions/categories/q-a) section.
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* For Slicer cochlea related bugs, please open a new [issue](https://github.com/MedicalImageAnalysisTutorials/SlicerCochlea/issues) if needed. Please mention your operating system, slicer version, and the error message you see in python interactor.
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* For sharing private information, dataset, a future project proposal or cooperation, please use the [email](ibr_ex@yahoo.com), use SlicerCochlea in the subject.
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* It would be nice to share your anonymised cochlea dataset.
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* It would be nice to contribute to this repository!

‎docs/elastixPars/parCochReg.txt‎

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(FixedInternalImagePixelType "short")
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(MovingInternalImagePixelType "short")
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(UseDirectionCosines "true")
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(Registration "MultiResolutionRegistration")
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(ResampleInterpolator "FinalBSplineInterpolator")
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(Resampler "DefaultResampler")
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(FixedImagePyramid "FixedRecursiveImagePyramid")
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(MovingImagePyramid "MovingRecursiveImagePyramid")
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(Interpolator "LinearInterpolator")
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(Optimizer "QuasiNewtonLBFGS")
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(Transform "EulerTransform")
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(Metric "AdvancedMattesMutualInformation")
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(NumberOfHistogramBins 16)
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(NumberOfResolutions 1)
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(MaximumNumberOfIterations 100)
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(NumberOfSpatialSamples 3000)
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(NewSamplesEveryIteration "true")
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(ImageSampler "RandomCoordinate")
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(ErodeMask "false")
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(AutomaticScalesEstimation "true")
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(AutomaticTransformInitialization "true")
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(AutomaticTransformInitializationMethod "GeomteryTop")
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(HowToCombineTransforms "Compose")
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(RequiredRatioOfValidSamples 0.01)
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(BSplineInterpolationOrder 1)
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(FinalBSplineInterpolationOrder 0)
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(DefaultPixelValue 0)
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(WriteResultImage "false")
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(ResultImagePixelType "short")
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(ResultImageFormat "nrrd")
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(WriteTransformParametersEachIteration "false")
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(WriteTransformParametersEachResolution "false")
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(WriteResultImageAfterEachIteration "false")
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(WriteResultImageAfterEachResolution "false")

‎docs/elastixPars/parCochSeg.txt‎

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(FixedInternalImagePixelType "short")
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(MovingInternalImagePixelType "short")
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(UseDirectionCosines "true")
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(Registration "MultiResolutionRegistration")
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(ResampleInterpolator "FinalBSplineInterpolator")
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(Resampler "DefaultResampler")
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(FixedImagePyramid "FixedRecursiveImagePyramid")
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(MovingImagePyramid "MovingRecursiveImagePyramid")
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(Interpolator "LinearInterpolator")
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(Optimizer "AdaptiveStochasticGradientDescent")
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(Transform "EulerTransform")
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(Metric "AdvancedMattesMutualInformation")
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(NumberOfHistogramBins 16)
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(NumberOfResolutions 1)
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(MaximumNumberOfIterations 500)
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(MaximumStepLength 1.0)
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(NumberOfSpatialSamples 3000)
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(NewSamplesEveryIteration "true")
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(ImageSampler "RandomCoordinate")
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(ErodeMask "false")
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(AutomaticScalesEstimation "true")
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(AutomaticTransformInitialization "true")
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(AutomaticTransformInitializationMethod "GeomteryTop")
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(HowToCombineTransforms "Compose")
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(RequiredRatioOfValidSamples 0.01)
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(BSplineInterpolationOrder 1)
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(FinalBSplineInterpolationOrder 0)
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(DefaultPixelValue 0)
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(WriteResultImage "true")
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(ResultImagePixelType "short")
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(ResultImageFormat "nrrd")
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(WriteTransformParametersEachIteration "false")
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(WriteTransformParametersEachResolution "false")
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(WriteResultImageAfterEachIteration "false")
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(WriteResultImageAfterEachResolution "false")

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