Files in stnava/ANTsR

ANTs in R: Quantification Tools for Biomedical Images

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ANTsR.Rproj

DESCRIPTION

Dockerfile

LICENSE

NAMESPACE

NEWS

R/ANTsR-package.R R/aaa_data.R R/abpBrainExtraction.R R/abpN4.R R/addNoiseToImage.R R/alff.R R/antsAffineInitializer.R R/antsApplyTransforms.R R/antsApplyTransformsToPoints.R R/antsAverageImages.R R/antsBOLDNetworkAnalysis.R R/antsCopyImageInfo.R R/antsImageClone.R R/antsImageHeaderInfo.R R/antsImageIterator_class.R R/antsImageMutualInformation.R R/antsImagePhysicalSpaceConsistency.R R/antsImageRead.R R/antsImageStats.R R/antsImageTypeCast.R R/antsImageWrite.R R/antsImage_class.R R/antsMatrix.R R/antsMotionCalculation.R R/antsMotionCorr.R R/antsMotionCorrStats.R R/antsRegistration.R R/antsSpatialICAfMRI.R R/antsTransformPoints.R R/antsVersions.R R/ants_brain_extraction.R R/ants_motion_estimation.R R/ants_set_get.R R/ants_set_seed.R R/antsrMetric_class.R R/antsrMotionCalculation.R R/antsrSurf.R R/antsrTransform_class.R R/antsr_resting_state_corr_eigenanat.R R/antsrimpute.R R/apply.antsImage.R R/aslAveraging.R R/aslCensoring.R R/aslDenoiseR.R R/aslPerfusion.R R/atropos.R R/basicInPaint.R R/bayesianCBF.R R/bayesianlm.R R/bigLMStats.R R/binarizeSNPs.R R/blockStimulus.R R/bloodPerfusionSVD.R R/bracket_assign.R R/bracket_subset.R R/check_ants.R R/clusterTimeSeries.R R/coerce_mask.R R/combineNuisancePredictors.R R/compcor.R R/composeDisplacementFields.R R/composeTransformsToField.R R/conjGradS.R R/convolveImage.R R/corw.R R/createJacobianDeterminantImage.R R/createWarpedGrid.R R/cropImage.R R/crossvalidatedR2.R R/cvEigenanatomy.R R/denoiseImage.R R/eanatDef.R R/eigSeg.R R/error_not_antsImage.R R/estSmooth.R R/euler.R R/exemplarInpainting.R R/extractDenseNetwork.R R/fastMarchingExtension.R R/filterfMRIforNetworkAnalysis.R R/fitBsplineDisplacementField.R R/fitBsplineObjectToScatteredData.R R/fitThinPlateSplineDisplacementField.R R/flags.R R/frequencyFilterfMRI.R R/fsl2antsrTransform.R R/functionalLungSegmentation.R R/fuzzySpatialCMeansSegmentation.R R/geoSeg.R R/getANTsRData.R R/getASLNoisePredictors.R R/getAverageOfTimeSeries.R R/getCentroids.R R/getMask.R R/getMultivariateTemplateCoordinates.R R/getNeighborhood.R R/getNetwork.R R/getTemplateCoordinates.R R/get_perfusion_predictors.R R/getfMRInuisanceVariables.R R/hausdorffDistance.R R/hemodynamicRF.R R/hist.antsImage.R R/histogramEqualizeImage.R R/histogramMatchImage.R R/iBind.R R/iMath.R R/iMathOps.R R/icawhiten.R R/image2ClusterImages.R R/imageFileNames2ImageList.R R/imageListToMatrix.R R/imageSimilarity.R R/imagesToMatrix.R R/initializeEigenanatomy.R R/int_antsExtractXptrAsString.R R/int_antsProcessArguments.R R/integrateVelocityField.R R/interleaveMatrixWithItself.R R/invertDisplacementField.R R/jlfPropagation.R R/joinEigenanatomy.R R/jointLabelFusion.R R/kellyKapowski.R R/kmeansSegmentation.R R/labelClusters.R R/labelGeometryMeasures.R R/labelImageCentroids.R R/labelOverlapMeasures.R R/labelStats.R R/labels2matrix.R R/landmarkTransforms.R R/lappend.R R/make3ViewPNG.R R/makeDiffGraph.R R/makeGraph.R R/makeImage.R R/makePowersPointsImage.R R/maskImage.R

R/maskImage_import.R

R/matrix2timeseries.R R/matrixToImages.R R/mergeChannels.R R/mergeLabels.R R/mni2tal.R R/morphology.R R/mrvnrfs.R R/multiLabelMorphology.R R/multiResRandomForestRegression.R R/multichannelPCA.R R/multiscaleSVDxpts.R R/n3BiasFieldCorrection.R R/n4BiasFieldCorrection.R R/networkCorrelation.R R/networkCovariance.R R/networkEiganat.R R/networkOverlap.R R/pairwiseImageDistanceMatrix.R R/partialVolumeCorrection.R R/perfusionregression.R R/petSUVR.R R/plot.antsImage.R R/plotBasicNetwork.R R/plotPrettyGraph.R R/powersACTrsfMRIprocessing.R R/preprocessRestingBOLD.R R/preprocessfMRI.R R/priorBasedSegmentation.R R/quantifyCBF.R R/quantifySNPs.R R/randomMask.R R/randsccan.R R/rankIntensity.R R/rapidlyInspectImageData.R R/reduceNetwork.R R/reflectImage.R R/regressProjections.R R/reho.R R/renormalizeProbabilityImages.R R/reorientImage.R R/resampleImage.R R/resampleImageToTarget.R R/resels.R R/rfSegmentation.R R/rftPval.R R/rftResults.R R/rimgs.R R/ripmmarc.R R/robustMatrixTransform.R R/rsfDenoise.R R/save.ANTsR.R R/segmentShapeFromImage.R R/segmentationRefinement.R R/simulateDisplacementField.R R/skeletonize.R R/smoothImage.R R/snapColors.R R/sparseDecom.R R/sparseDecom2.R R/sparseDecom2boot.R R/sparseDecomboot.R R/sparseRegression.R R/spatialbayesianlm.R R/splitChannels.R R/splitData.R R/splitNDImageToList.R R/statFieldThresh.R R/subgradientL1Regression.R R/subjectDataToGroupDataFrame.R R/summarizeClusters.R R/taskFMRI.R R/temporalwhiten.R R/thresholdImage.R R/timeseries2matrix.R R/timeseriesN3.R R/timeserieswindow2matrix.R R/usePkg.R R/vwnrfs.R R/weingartenImageCurvature.R R/whiten.R R/writeNormalizedPopulationData.R R/zzz.R R/zzz_Arith.R R/zzz_Comparison.R R/zzz_Logic.R R/zzz_Math.R R/zzz_Summary.R R/zzz_accessors.R R/zzz_finite.R R/zzz_which.R README.md code_of_conduct.md data-raw/mutli_component_image.R

data/.Rapp.history

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man/ANTsR.Rd man/DesikanKillianyTourville.Rd man/aal.Rd man/abpBrainExtraction.Rd man/abpN4.Rd man/accessor-methods.Rd man/addNoiseToImage.Rd man/affineInitializer.Rd man/alffmap.Rd man/ants.set.seed.Rd man/antsApplyTransforms.Rd man/antsApplyTransformsToPoints.Rd man/antsAverageImages.Rd man/antsBOLDNetworkAnalysis.Rd man/antsCompileFlags.Rd man/antsCopyImageInfo.Rd man/antsCopyImageInfo2.Rd man/antsDir.Rd man/antsImage.Rd man/antsImageClone.Rd man/antsImageGetSet.Rd man/antsImageHeaderInfo.Rd man/antsImageIterator.Rd man/antsImageIteratorGet.Rd man/antsImageIteratorGetIndex.Rd man/antsImageIteratorGoToBegin.Rd man/antsImageIteratorGoToReverseBegin.Rd man/antsImageIteratorIsAtEnd.Rd man/antsImageIteratorIsAtReverseEnd.Rd man/antsImageIteratorNext.Rd man/antsImageIteratorPrevious.Rd man/antsImageIteratorRemaining.Rd man/antsImageIteratorSet.Rd man/antsImageIteratorSetIndex.Rd man/antsImageIterator_class.Rd man/antsImageMutualInformation.Rd man/antsImagePhysicalSpaceConsistency.Rd man/antsImageRead.Rd man/antsImageSummary.Rd man/antsImageTypeCast.Rd man/antsImageWrite.Rd man/antsImagemath.Rd man/antsImageops.Rd man/antsIncludes.Rd man/antsLibs.Rd man/antsMatrix_class.Rd man/antsMotionCalculation.Rd man/antsMotionCorr.Rd man/antsRegion-class.Rd man/antsRegistration.Rd man/antsSetPixels.Rd man/antsSpatialICAfMRI.Rd man/antsTransformIndexToPhysicalPoint.Rd man/antsTransformPhysicalPointToIndex.Rd man/antsVersions.Rd man/antsrGetPointerName.Rd man/antsrMetric.Rd man/antsrMetricCreate.Rd man/antsrMetricGetDerivative.Rd man/antsrMetricGetValue.Rd man/antsrMetricInitialize.Rd man/antsrMetricSetFixedImage.Rd man/antsrMetricSetFixedImageMask.Rd man/antsrMetricSetFixedTransform.Rd man/antsrMetricSetMovingImage.Rd man/antsrMetricSetMovingImageMask.Rd man/antsrMetricSetMovingTransform.Rd man/antsrMetricSetNumberOfHistogramBins.Rd man/antsrMetricSetRadius.Rd man/antsrMetricSetSampling.Rd man/antsrMotionCalculation.Rd man/antsrSurf.Rd man/antsrTransform.Rd man/antsrTransformFromDisplacementField.Rd man/antsrVersions.Rd man/antsrVol.Rd man/antsrimpute.Rd man/apply.Rd man/applyAntsrTransform.Rd man/applyAntsrTransformToImage.Rd man/applyAntsrTransformToPoint.Rd man/applyAntsrTransformToVector.Rd man/as.antsImage.Rd man/as.antsMatrix.Rd man/as.array.Rd man/aslAveraging.Rd man/aslCensoring.Rd man/aslDenoiseR.Rd man/aslPerfusion.Rd man/atropos.Rd man/basicInPaint.Rd man/bayesianCBF.Rd man/bayesianlm.Rd man/bigLMStats.Rd man/blockStimulus.Rd man/bloodPerfusionSVD.Rd man/bold_correlation_matrix.Rd man/boxplot.antsImage.Rd man/brackets.Rd man/buildTemplate.Rd man/check_ants-methods.Rd man/clusterTimeSeries.Rd man/coerce_mask.Rd man/combineNuisancePredictors.Rd man/compcor.Rd man/composeAntsrTransforms.Rd man/composeDisplacementFields.Rd man/composeTransformsToField.Rd man/computeDVARS.Rd man/computeDVARSspatialMap.Rd man/convolveImage.Rd man/corw.Rd man/createAntsrTransform.Rd man/createJacobianDeterminantImage.Rd man/createWarpedGrid.Rd man/cropImage.Rd man/cropIndices.Rd man/crossvalidatedR2.Rd man/cut.antsImage.Rd man/cvEigenanatomy.Rd man/deconvolutionSVD.Rd man/decropImage.Rd man/denoiseImage.Rd man/density.antsImage.Rd man/displacementFieldFromAntsrTransform.Rd man/eanatDef.Rd man/eanatSelect.Rd man/eigSeg.Rd man/error_not_antsImage.Rd man/estSmooth.Rd man/euler.Rd man/exemplarInpainting.Rd man/extractSlice.Rd man/fMRINormalization.Rd man/fastMarchingExtension.Rd man/filterfMRIforNetworkAnalysis.Rd man/fitBsplineDisplacementField.Rd man/fitBsplineObjectToScatteredData.Rd man/fitThinPlateSplineDisplacementField.Rd man/fitTimeVaryingTransformToPointSets.Rd man/fitTransformToPairedPoints.Rd man/frequencyFilterfMRI.Rd man/fsl2antsrTransform.Rd man/functionalLungSegmentation.Rd man/fuzzySpatialCMeansSegmentation.Rd man/generateAifMaskImage.Rd man/geoSeg.Rd man/getANTsRData.Rd man/getASLNoisePredictors.Rd man/getAntsrTransformFixedParameters.Rd man/getAntsrTransformParameters.Rd man/getAverageOfTimeSeries.Rd man/getCenterOfMass.Rd man/getCentroids.Rd man/getMask.Rd man/getMultiResFeatureMatrix.Rd man/getMultivariateTemplateCoordinates.Rd man/getNeighborhoodAtVoxel.Rd man/getNeighborhoodInMask.Rd man/getPixels.Rd man/getTemplateCoordinates.Rd man/getfMRInuisanceVariables.Rd man/grapes-greater-than-grapes.Rd man/hausdorffDistance.Rd man/hemodynamicRF.Rd man/hist.antsImage.Rd man/histogramEqualizeImage.Rd man/histogramMatchImage.Rd man/histogramMatchImage2.Rd man/iBind.Rd man/iMath.Rd man/iMathOps.Rd man/icawhiten.Rd man/ilr.Rd man/ilr.predict.Rd man/image2ClusterImages.Rd man/imageDomainToSpatialMatrix.Rd man/imageFileNames2ImageList.Rd man/imageListToMatrix.Rd man/imageSimilarity.Rd man/imagesToMatrix.Rd man/initializeEigenanatomy.Rd man/initializeSimlr.Rd man/int_antsProcessArguments.Rd man/integrateVectorField.Rd man/integrateVelocityField.Rd man/interleaveMatrixWithItself.Rd man/invertAntsrTransform.Rd man/invertDisplacementField.Rd man/is.antsImage.Rd man/jlfProp.Rd man/joinEigenanatomy.Rd man/jointLabelFusion.Rd man/jointSmoothMatrixReconstruction.Rd man/kellyKapowski.Rd man/kmeansSegmentation.Rd man/knnSmoothImage.Rd man/knnSmoothingMatrix.Rd man/labelClusters.Rd man/labelGeometryMeasures.Rd man/labelImageCentroids.Rd man/labelOverlapMeasures.Rd man/labelStats.Rd man/labels2matrix.Rd man/lappend.Rd man/load.ANTsR.Rd man/localGyrificationIndex.Rd man/localJointLabelFusion.Rd man/lowrankRowMatrix.Rd man/make3ViewPNG.Rd man/makeGraph.Rd man/makeImage.Rd man/makePointsImage.Rd man/makePowersPointsImage.Rd man/maskImage.Rd man/mask_values.Rd man/matrix2timeseries.Rd man/matrixToImages.Rd man/mean.Rd man/median.Rd man/mergeChannels.Rd man/mergeListToNDImage.Rd man/mild.Rd man/milr.Rd man/milr.predict.Rd man/mni2tal.Rd man/morphology.Rd man/motion_correction.Rd man/mrvnrfs.Rd man/mrvnrfs.predict.Rd man/multiLabelMorphology.Rd man/multiResRandomForestRegression.Rd man/multichannelPCA.Rd man/multichannelToVector.Rd man/multiscaleSVD.Rd man/n3BiasFieldCorrection.Rd man/n3BiasFieldCorrection2.Rd man/n4BiasFieldCorrection.Rd man/networkEiganat.Rd man/orthogonalizeAndQSparsify.Rd man/pairwiseImageDistanceMatrix.Rd man/partialVolumeCorrection.Rd man/perfusionregression.Rd man/petSUVR.Rd man/plot.antsImage.Rd man/plotBasicNetwork.Rd man/plotPrettyGraph.Rd man/powers_areal_mni_itk.Rd man/predictSimlr.Rd man/preprocessRestingBOLD.Rd man/preprocessfMRI.Rd man/priorBasedSegmentation.Rd man/quantifyCBF.Rd man/quantifySNPs.Rd man/quantile.antsImage.Rd man/randcca.Rd man/randomMask.Rd man/randsvd.Rd man/randwhiten.Rd man/rankBasedMatrixSegmentation.Rd man/rankIntensity.Rd man/rapidlyInspectImageData.Rd man/readAntsrTransform.Rd man/readNormalizedPopulationData.Rd man/reflectImage.Rd man/reflectionMatrix.Rd man/regressProjections.Rd man/regularizeSimlr.Rd man/reho.Rd man/renormalizeProbabilityImages.Rd man/reorientImage.Rd man/resampleImage.Rd man/resampleImageToTarget.Rd man/resels.Rd man/rfSegmentation.Rd man/rfSegmentationPredict.Rd man/rftPval.Rd man/rftResults.Rd man/ri.Rd man/robustMatrixTransform.Rd man/rsfDenoise.Rd man/save.ANTsR.Rd man/sd.Rd man/segmentShapeFromImage.Rd man/segmentationRefinement.predict.Rd man/segmentationRefinement.train.Rd man/setAntsrTransformFixedParameters.Rd man/setAntsrTransformParameters.Rd man/simlr.Rd man/simlrU.Rd man/simulateDisplacementField.Rd man/skeletonize.Rd man/smoothAppGradCCA.Rd man/smoothImage.Rd man/smoothMatrixPrediction.Rd man/smoothMultiRegression.Rd man/smoothRegression.Rd man/sparseDecom.Rd man/sparseDecom2.Rd man/sparseDecom2boot.Rd man/sparseDecomboot.Rd man/sparseDistanceMatrix.Rd man/sparseDistanceMatrixXY.Rd man/sparseRegression.Rd man/spatialbayesianlm.Rd man/splitChannels.Rd man/splitData.Rd man/splitMask.Rd man/splitNDImageToList.Rd man/statFieldThresh.Rd man/subgradientL1Regression.Rd man/subjectDataToGroupDataFrame.Rd man/subset.Rd man/taskFMRI.Rd man/temporalwhiten.Rd man/testEanat.Rd man/thresholdImage.Rd man/timeseries2matrix.Rd man/timeseriesN3.Rd man/timeserieswindow2matrix.Rd man/tracts.Rd man/trapz.Rd man/unique.Rd man/usePkg.Rd man/var.Rd man/vectorToMultichannel.Rd man/vwnrfs.Rd man/vwnrfs.predict.Rd man/weingartenImageCurvature.Rd man/whiten.Rd man/writeAntsrTransform.Rd man/writeNormalizedPopulationData.Rd tests/testthat.R

tests/testthat/output.nii.gz

tests/testthat/test-Atropos.R tests/testthat/test-antsImage.R tests/testthat/test-antsImageClone.R tests/testthat/test-antsImageRead.R tests/testthat/test-antsImageWrite.R tests/testthat/test-iMath.R

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.