From f7191d81e0762eae56e7418b6950438746af1229 Mon Sep 17 00:00:00 2001 From: stnava Date: Sun, 11 Aug 2024 10:50:10 -0400 Subject: [PATCH] DOC: updated site --- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 4 +- docs/articles/simlr_interpretation.html | 783 +++++++++++++++++- docs/authors.html | 2 +- docs/code_of_conduct.html | 2 +- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/ANTsR.html | 2 +- docs/reference/DesikanKillianyTourville.html | 2 +- docs/reference/aal.html | 2 +- docs/reference/abpBrainExtraction.html | 2 +- docs/reference/abpN4.html | 2 +- docs/reference/accessor-methods.html | 2 +- docs/reference/addNoiseToImage.html | 2 +- docs/reference/adjusted_rvcoef.html | 4 +- docs/reference/affineInitializer.html | 2 +- docs/reference/alffmap.html | 2 +- docs/reference/ants.set.seed.html | 2 +- docs/reference/antsApplyTransforms.html | 28 +- .../antsApplyTransformsToPoints.html | 2 +- docs/reference/antsAverageImages.html | 2 +- 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2 +- .../subjectDataToGroupDataFrame.html | 2 +- docs/reference/subset.html | 2 +- docs/reference/take_abs_unsigned.html | 2 +- docs/reference/taskFMRI.html | 2 +- docs/reference/temporalwhiten.html | 2 +- docs/reference/testEanat.html | 2 +- docs/reference/thresholdImage.html | 2 +- docs/reference/timeseries2matrix.html | 2 +- docs/reference/timeseriesN3.html | 2 +- docs/reference/timeserieswindow2matrix.html | 2 +- docs/reference/tracts.html | 2 +- docs/reference/trapz.html | 2 +- docs/reference/unique.html | 2 +- docs/reference/usePkg.html | 2 +- docs/reference/var.html | 2 +- docs/reference/vectorToMultichannel.html | 4 +- docs/reference/vector_to_df.html | 2 +- .../visualize_lowrank_relationships.html | 2 +- docs/reference/vwnrfs.html | 2 +- docs/reference/vwnrfs.predict.html | 2 +- docs/reference/weingartenImageCurvature.html | 2 +- docs/reference/whiten.html | 2 +- docs/reference/whiten_matrix.html | 2 +- docs/reference/writeAntsrTransform.html | 2 +- .../writeNormalizedPopulationData.html | 2 +- docs/sitemap.xml | 48 ++ 362 files changed, 1275 insertions(+), 432 deletions(-) diff --git a/docs/404.html b/docs/404.html index a2355494..42e492fc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -49,7 +49,7 @@ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index af4e4e2a..88ac0aec 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -32,7 +32,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index 91b59049..503d3180 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -32,7 +32,7 @@ @@ -51,7 +51,7 @@

Articles

All vignettes

-
SiMLR interpretation
+
simlr_interpretation
diff --git a/docs/articles/simlr_interpretation.html b/docs/articles/simlr_interpretation.html index be1079a0..7f652166 100644 --- a/docs/articles/simlr_interpretation.html +++ b/docs/articles/simlr_interpretation.html @@ -5,13 +5,13 @@ -SiMLR interpretation • ANTsR +simlr_interpretation • ANTsR - + diff --git a/docs/code_of_conduct.html b/docs/code_of_conduct.html index 43f65bcb..cb795c4f 100644 --- a/docs/code_of_conduct.html +++ b/docs/code_of_conduct.html @@ -32,7 +32,7 @@ diff --git a/docs/index.html b/docs/index.html index 6f32fd79..60c1579a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -57,7 +57,7 @@ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f590948e..b7200423 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: simlr_interpretation: simlr_interpretation.html -last_built: 2024-08-11T12:30Z +last_built: 2024-08-11T14:40Z diff --git a/docs/reference/ANTsR.html b/docs/reference/ANTsR.html index 3e22a77c..da712bb1 100644 --- a/docs/reference/ANTsR.html +++ b/docs/reference/ANTsR.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/DesikanKillianyTourville.html b/docs/reference/DesikanKillianyTourville.html index 78e7eb15..47e30c01 100644 --- a/docs/reference/DesikanKillianyTourville.html +++ b/docs/reference/DesikanKillianyTourville.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/aal.html b/docs/reference/aal.html index 80a436a0..44bb5732 100644 --- a/docs/reference/aal.html +++ b/docs/reference/aal.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/abpBrainExtraction.html b/docs/reference/abpBrainExtraction.html index b75886aa..64bc9140 100644 --- a/docs/reference/abpBrainExtraction.html +++ b/docs/reference/abpBrainExtraction.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/abpN4.html b/docs/reference/abpN4.html index 495021ac..346c4b53 100644 --- a/docs/reference/abpN4.html +++ b/docs/reference/abpN4.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/accessor-methods.html b/docs/reference/accessor-methods.html index 2a815efd..b1ce8145 100644 --- a/docs/reference/accessor-methods.html +++ b/docs/reference/accessor-methods.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/addNoiseToImage.html b/docs/reference/addNoiseToImage.html index efa974d4..c0be39be 100644 --- a/docs/reference/addNoiseToImage.html +++ b/docs/reference/addNoiseToImage.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/adjusted_rvcoef.html b/docs/reference/adjusted_rvcoef.html index 45d97ad3..9b87fe86 100644 --- a/docs/reference/adjusted_rvcoef.html +++ b/docs/reference/adjusted_rvcoef.html @@ -32,7 +32,7 @@ @@ -87,7 +87,7 @@

Examples

X <- matrix(rnorm(100), nrow = 10)
 Y <- matrix(rnorm(100), nrow = 10)
 adjusted_rvcoef(X, Y)
-#> [1] 0.1024623
+#> [1] 0.1249435
diff --git a/docs/reference/affineInitializer.html b/docs/reference/affineInitializer.html index 925bd9d2..5b04baeb 100644 --- a/docs/reference/affineInitializer.html +++ b/docs/reference/affineInitializer.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/alffmap.html b/docs/reference/alffmap.html index 67d6d355..7ff05776 100644 --- a/docs/reference/alffmap.html +++ b/docs/reference/alffmap.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/ants.set.seed.html b/docs/reference/ants.set.seed.html index 26fa36f6..6e77e4b0 100644 --- a/docs/reference/ants.set.seed.html +++ b/docs/reference/ants.set.seed.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsApplyTransforms.html b/docs/reference/antsApplyTransforms.html index 9b31aeb3..6ff68e05 100644 --- a/docs/reference/antsApplyTransforms.html +++ b/docs/reference/antsApplyTransforms.html @@ -38,7 +38,7 @@ @@ -167,7 +167,7 @@

Examples

fixed = fixed, moving = moving, typeofTransform = "SyN", verbose = TRUE, printArgs = TRUE ) -#> antsRegistration -d 2 -r [0x600001d04440,0x600001d04470,1] -m mattes[0x600001d04440,0x600001d04470,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x0 -s 3x2x1x0 -f 4x2x2x1 -x [NA,NA] -m mattes[0x600001d04440,0x600001d04470,1,32] -t SyN[0.2,3,0] -c [ 40x20x0 ,1e-7,8] -s 2x1x0 -f 4x2x1 -u 0 -z 1 -o [/tmp//RtmptUdSss/file851afe3f0a6,0x600001d04570,0x600001d040f0] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 -v 1 +#> antsRegistration -d 2 -r [0x600002ec4640,0x600002ec4970,1] -m mattes[0x600002ec4640,0x600002ec4970,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x0 -s 3x2x1x0 -f 4x2x2x1 -x [NA,NA] -m mattes[0x600002ec4640,0x600002ec4970,1,32] -t SyN[0.2,3,0] -c [ 40x20x0 ,1e-7,8] -s 2x1x0 -f 4x2x1 -u 0 -z 1 -o [/tmp//Rtmp2miWxn/file8ddc4c7b7e92,0x600002ec4aa0,0x600002ec4b10] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 -v 1 mywarpedimage <- antsApplyTransforms( fixed = fixed, moving = moving, transformlist = mytx$fwdtransforms @@ -185,18 +185,18 @@

Examples

transformlist = mytx$fwdtransforms[2], whichtoinvert = 1, verbose = TRUE ) -#> [1] "-d" -#> [2] "2" -#> [3] "-i" -#> [4] "<pointer: 0x600001d042c0>" -#> [5] "-o" -#> [6] "<pointer: 0x600001d2c020>" -#> [7] "-r" -#> [8] "<pointer: 0x600001d22c10>" -#> [9] "-n" -#> [10] "linear" -#> [11] "-t" -#> [12] "[/tmp//RtmptUdSss/file851afe3f0a60GenericAffine.mat,1]" +#> [1] "-d" +#> [2] "2" +#> [3] "-i" +#> [4] "<pointer: 0x600002ec4a60>" +#> [5] "-o" +#> [6] "<pointer: 0x600002ec3990>" +#> [7] "-r" +#> [8] "<pointer: 0x600002ed3790>" +#> [9] "-n" +#> [10] "linear" +#> [11] "-t" +#> [12] "[/tmp//Rtmp2miWxn/file8ddc4c7b7e920GenericAffine.mat,1]" cfile <- antsApplyTransforms( fixed = fixed, moving = moving, transformlist = mytx$fwdtransforms, diff --git a/docs/reference/antsApplyTransformsToPoints.html b/docs/reference/antsApplyTransformsToPoints.html index fe3dbbf1..6b5ece62 100644 --- a/docs/reference/antsApplyTransformsToPoints.html +++ b/docs/reference/antsApplyTransformsToPoints.html @@ -40,7 +40,7 @@ diff --git a/docs/reference/antsAverageImages.html b/docs/reference/antsAverageImages.html index 6effdc4b..5ec62148 100644 --- a/docs/reference/antsAverageImages.html +++ b/docs/reference/antsAverageImages.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsBOLDNetworkAnalysis.html b/docs/reference/antsBOLDNetworkAnalysis.html index 73c9c570..1d0de639 100644 --- a/docs/reference/antsBOLDNetworkAnalysis.html +++ b/docs/reference/antsBOLDNetworkAnalysis.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/antsCompileFlags.html b/docs/reference/antsCompileFlags.html index 4f9dd597..0cb93f33 100644 --- a/docs/reference/antsCompileFlags.html +++ b/docs/reference/antsCompileFlags.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsCopyImageInfo.html b/docs/reference/antsCopyImageInfo.html index 440ee6a7..c5a5d6df 100644 --- a/docs/reference/antsCopyImageInfo.html +++ b/docs/reference/antsCopyImageInfo.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsCopyImageInfo2.html b/docs/reference/antsCopyImageInfo2.html index 47f9ce9c..4c4b002a 100644 --- a/docs/reference/antsCopyImageInfo2.html +++ b/docs/reference/antsCopyImageInfo2.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/antsDir.html b/docs/reference/antsDir.html index 910ac18d..95eaaf77 100644 --- a/docs/reference/antsDir.html +++ b/docs/reference/antsDir.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImage.html b/docs/reference/antsImage.html index 7cc2851d..4fcd5c5b 100644 --- a/docs/reference/antsImage.html +++ b/docs/reference/antsImage.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/antsImageClone.html b/docs/reference/antsImageClone.html index 196bcc5e..9438e3f5 100644 --- a/docs/reference/antsImageClone.html +++ b/docs/reference/antsImageClone.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/antsImageGetSet.html b/docs/reference/antsImageGetSet.html index 31f7349f..09718ddb 100644 --- a/docs/reference/antsImageGetSet.html +++ b/docs/reference/antsImageGetSet.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageHeaderInfo.html b/docs/reference/antsImageHeaderInfo.html index d7463f08..eb069bd6 100644 --- a/docs/reference/antsImageHeaderInfo.html +++ b/docs/reference/antsImageHeaderInfo.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIterator.html b/docs/reference/antsImageIterator.html index 60041314..f7e05766 100644 --- a/docs/reference/antsImageIterator.html +++ b/docs/reference/antsImageIterator.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorGet.html b/docs/reference/antsImageIteratorGet.html index ee6f0ecb..9e024cd9 100644 --- a/docs/reference/antsImageIteratorGet.html +++ b/docs/reference/antsImageIteratorGet.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorGetIndex.html b/docs/reference/antsImageIteratorGetIndex.html index e76a3832..bfd3d8f8 100644 --- a/docs/reference/antsImageIteratorGetIndex.html +++ b/docs/reference/antsImageIteratorGetIndex.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorGoToBegin.html b/docs/reference/antsImageIteratorGoToBegin.html index c985b4f1..f366d2eb 100644 --- a/docs/reference/antsImageIteratorGoToBegin.html +++ b/docs/reference/antsImageIteratorGoToBegin.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorGoToReverseBegin.html b/docs/reference/antsImageIteratorGoToReverseBegin.html index c767c85a..d903e627 100644 --- a/docs/reference/antsImageIteratorGoToReverseBegin.html +++ b/docs/reference/antsImageIteratorGoToReverseBegin.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorIsAtEnd.html b/docs/reference/antsImageIteratorIsAtEnd.html index db7fcae2..8d86b0fe 100644 --- a/docs/reference/antsImageIteratorIsAtEnd.html +++ b/docs/reference/antsImageIteratorIsAtEnd.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorIsAtReverseEnd.html b/docs/reference/antsImageIteratorIsAtReverseEnd.html index fe04b404..0ea50121 100644 --- a/docs/reference/antsImageIteratorIsAtReverseEnd.html +++ b/docs/reference/antsImageIteratorIsAtReverseEnd.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorNext.html b/docs/reference/antsImageIteratorNext.html index 0d1d2d51..642c471b 100644 --- a/docs/reference/antsImageIteratorNext.html +++ b/docs/reference/antsImageIteratorNext.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorPrevious.html b/docs/reference/antsImageIteratorPrevious.html index 026dc86e..0363171e 100644 --- a/docs/reference/antsImageIteratorPrevious.html +++ b/docs/reference/antsImageIteratorPrevious.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorRemaining.html b/docs/reference/antsImageIteratorRemaining.html index b6231e9f..33eee4ca 100644 --- a/docs/reference/antsImageIteratorRemaining.html +++ b/docs/reference/antsImageIteratorRemaining.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorSet.html b/docs/reference/antsImageIteratorSet.html index 547cbfc1..f16f261d 100644 --- a/docs/reference/antsImageIteratorSet.html +++ b/docs/reference/antsImageIteratorSet.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIteratorSetIndex.html b/docs/reference/antsImageIteratorSetIndex.html index 52b39bce..6d691a97 100644 --- a/docs/reference/antsImageIteratorSetIndex.html +++ b/docs/reference/antsImageIteratorSetIndex.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageIterator_class.html b/docs/reference/antsImageIterator_class.html index fa6f7f77..7e14cc49 100644 --- a/docs/reference/antsImageIterator_class.html +++ b/docs/reference/antsImageIterator_class.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/antsImageMutualInformation.html b/docs/reference/antsImageMutualInformation.html index f3b7b21e..d3463a58 100644 --- a/docs/reference/antsImageMutualInformation.html +++ b/docs/reference/antsImageMutualInformation.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImagePhysicalSpaceConsistency.html b/docs/reference/antsImagePhysicalSpaceConsistency.html index caa3674e..c8951319 100644 --- a/docs/reference/antsImagePhysicalSpaceConsistency.html +++ b/docs/reference/antsImagePhysicalSpaceConsistency.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageRead.html b/docs/reference/antsImageRead.html index 3d7d751d..05f1c64c 100644 --- a/docs/reference/antsImageRead.html +++ b/docs/reference/antsImageRead.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageSummary.html b/docs/reference/antsImageSummary.html index a76f1e5b..265ba2a2 100644 --- a/docs/reference/antsImageSummary.html +++ b/docs/reference/antsImageSummary.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageTypeCast.html b/docs/reference/antsImageTypeCast.html index c7bb226d..58d64abf 100644 --- a/docs/reference/antsImageTypeCast.html +++ b/docs/reference/antsImageTypeCast.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageWrite.html b/docs/reference/antsImageWrite.html index ed64759e..0f4232b3 100644 --- a/docs/reference/antsImageWrite.html +++ b/docs/reference/antsImageWrite.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImagemath.html b/docs/reference/antsImagemath.html index 5a2032b3..becf172f 100644 --- a/docs/reference/antsImagemath.html +++ b/docs/reference/antsImagemath.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsImageops.html b/docs/reference/antsImageops.html index c7e1174b..ced3f9eb 100644 --- a/docs/reference/antsImageops.html +++ b/docs/reference/antsImageops.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsIncludes.html b/docs/reference/antsIncludes.html index 1fecdf93..b01bdf34 100644 --- a/docs/reference/antsIncludes.html +++ b/docs/reference/antsIncludes.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsLibs.html b/docs/reference/antsLibs.html index 72b31c87..0ece5bc1 100644 --- a/docs/reference/antsLibs.html +++ b/docs/reference/antsLibs.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsMatrix_class.html b/docs/reference/antsMatrix_class.html index 5ecb5311..6eae82ee 100644 --- a/docs/reference/antsMatrix_class.html +++ b/docs/reference/antsMatrix_class.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/antsMotionCalculation.html b/docs/reference/antsMotionCalculation.html index 078d23ee..3d8d35c9 100644 --- a/docs/reference/antsMotionCalculation.html +++ b/docs/reference/antsMotionCalculation.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsMotionCorr.html b/docs/reference/antsMotionCorr.html index 7c2c5679..6b815196 100644 --- a/docs/reference/antsMotionCorr.html +++ b/docs/reference/antsMotionCorr.html @@ -37,7 +37,7 @@ diff --git a/docs/reference/antsRegion-class.html b/docs/reference/antsRegion-class.html index 92bfb2a2..62d99294 100644 --- a/docs/reference/antsRegion-class.html +++ b/docs/reference/antsRegion-class.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsRegistration.html b/docs/reference/antsRegistration.html index 44dddbf7..853f6cf6 100644 --- a/docs/reference/antsRegistration.html +++ b/docs/reference/antsRegistration.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/antsSetPixels.html b/docs/reference/antsSetPixels.html index d98e7394..b61cfc22 100644 --- a/docs/reference/antsSetPixels.html +++ b/docs/reference/antsSetPixels.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsSpatialICAfMRI.html b/docs/reference/antsSpatialICAfMRI.html index b85520d9..9a76784f 100644 --- a/docs/reference/antsSpatialICAfMRI.html +++ b/docs/reference/antsSpatialICAfMRI.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/antsTransformIndexToPhysicalPoint.html b/docs/reference/antsTransformIndexToPhysicalPoint.html index 252163eb..b0c50c9f 100644 --- a/docs/reference/antsTransformIndexToPhysicalPoint.html +++ b/docs/reference/antsTransformIndexToPhysicalPoint.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsTransformPhysicalPointToIndex.html b/docs/reference/antsTransformPhysicalPointToIndex.html index 3243eafb..1b25aa0a 100644 --- a/docs/reference/antsTransformPhysicalPointToIndex.html +++ b/docs/reference/antsTransformPhysicalPointToIndex.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsVersions.html b/docs/reference/antsVersions.html index 7b7ecd92..d42c73cd 100644 --- a/docs/reference/antsVersions.html +++ b/docs/reference/antsVersions.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/antsrGetPointerName.html b/docs/reference/antsrGetPointerName.html index 5efc3b5d..463e21c3 100644 --- a/docs/reference/antsrGetPointerName.html +++ b/docs/reference/antsrGetPointerName.html @@ -33,7 +33,7 @@ @@ -81,9 +81,9 @@

Examples


 img <- antsImageRead(getANTsRData("r16"))
 antsrGetPointerName(img)
-#> [1] "0x600001c4b280"
+#> [1] "0x600002ec84e0"
 antsrGetPointerName(antsImageClone(img))
-#> [1] "0x600001c4b860"
+#> [1] "0x600002ec8690"
diff --git a/docs/reference/antsrMetric.html b/docs/reference/antsrMetric.html index d68c6757..42d8201a 100644 --- a/docs/reference/antsrMetric.html +++ b/docs/reference/antsrMetric.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricCreate.html b/docs/reference/antsrMetricCreate.html index 47bbd42f..86056d71 100644 --- a/docs/reference/antsrMetricCreate.html +++ b/docs/reference/antsrMetricCreate.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricGetDerivative.html b/docs/reference/antsrMetricGetDerivative.html index c7c21089..f7d949fa 100644 --- a/docs/reference/antsrMetricGetDerivative.html +++ b/docs/reference/antsrMetricGetDerivative.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricGetValue.html b/docs/reference/antsrMetricGetValue.html index d229e5bb..08de380b 100644 --- a/docs/reference/antsrMetricGetValue.html +++ b/docs/reference/antsrMetricGetValue.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricInitialize.html b/docs/reference/antsrMetricInitialize.html index 7e249551..92605e45 100644 --- a/docs/reference/antsrMetricInitialize.html +++ b/docs/reference/antsrMetricInitialize.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetFixedImage.html b/docs/reference/antsrMetricSetFixedImage.html index 2596759e..586699ad 100644 --- a/docs/reference/antsrMetricSetFixedImage.html +++ b/docs/reference/antsrMetricSetFixedImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetFixedImageMask.html b/docs/reference/antsrMetricSetFixedImageMask.html index 35ee0474..e3c581e7 100644 --- a/docs/reference/antsrMetricSetFixedImageMask.html +++ b/docs/reference/antsrMetricSetFixedImageMask.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetFixedTransform.html b/docs/reference/antsrMetricSetFixedTransform.html index 3825356c..7a8c93ec 100644 --- a/docs/reference/antsrMetricSetFixedTransform.html +++ b/docs/reference/antsrMetricSetFixedTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetMovingImage.html b/docs/reference/antsrMetricSetMovingImage.html index 37ddae53..ab0b2a77 100644 --- a/docs/reference/antsrMetricSetMovingImage.html +++ b/docs/reference/antsrMetricSetMovingImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetMovingImageMask.html b/docs/reference/antsrMetricSetMovingImageMask.html index 0ee11ed5..aca27fe2 100644 --- a/docs/reference/antsrMetricSetMovingImageMask.html +++ b/docs/reference/antsrMetricSetMovingImageMask.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetMovingTransform.html b/docs/reference/antsrMetricSetMovingTransform.html index 9ef887ea..cf8b50fd 100644 --- a/docs/reference/antsrMetricSetMovingTransform.html +++ b/docs/reference/antsrMetricSetMovingTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetNumberOfHistogramBins.html b/docs/reference/antsrMetricSetNumberOfHistogramBins.html index a75f755f..0e08783c 100644 --- a/docs/reference/antsrMetricSetNumberOfHistogramBins.html +++ b/docs/reference/antsrMetricSetNumberOfHistogramBins.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetRadius.html b/docs/reference/antsrMetricSetRadius.html index dba10f4b..b862a73c 100644 --- a/docs/reference/antsrMetricSetRadius.html +++ b/docs/reference/antsrMetricSetRadius.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMetricSetSampling.html b/docs/reference/antsrMetricSetSampling.html index 4933a5b8..680bdc5a 100644 --- a/docs/reference/antsrMetricSetSampling.html +++ b/docs/reference/antsrMetricSetSampling.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrMotionCalculation.html b/docs/reference/antsrMotionCalculation.html index 395cc5c6..129106df 100644 --- a/docs/reference/antsrMotionCalculation.html +++ b/docs/reference/antsrMotionCalculation.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrSurf.html b/docs/reference/antsrSurf.html index 06e0c319..0610efd2 100644 --- a/docs/reference/antsrSurf.html +++ b/docs/reference/antsrSurf.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/antsrTransform.html b/docs/reference/antsrTransform.html index fb7bd861..9a1bfd8e 100644 --- a/docs/reference/antsrTransform.html +++ b/docs/reference/antsrTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrTransformFromDisplacementField.html b/docs/reference/antsrTransformFromDisplacementField.html index 58ac1fc5..e5957051 100644 --- a/docs/reference/antsrTransformFromDisplacementField.html +++ b/docs/reference/antsrTransformFromDisplacementField.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/antsrVersions.html b/docs/reference/antsrVersions.html index 14c89024..75cb22c5 100644 --- a/docs/reference/antsrVersions.html +++ b/docs/reference/antsrVersions.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/antsrVol.html b/docs/reference/antsrVol.html index ccc5efeb..90c46901 100644 --- a/docs/reference/antsrVol.html +++ b/docs/reference/antsrVol.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/antsrimpute.html b/docs/reference/antsrimpute.html index ccb820e1..860486e7 100644 --- a/docs/reference/antsrimpute.html +++ b/docs/reference/antsrimpute.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/apply.html b/docs/reference/apply.html index a8b746f0..369ff2c5 100644 --- a/docs/reference/apply.html +++ b/docs/reference/apply.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/applyAntsrTransform.html b/docs/reference/applyAntsrTransform.html index 6319af18..12bdc6be 100644 --- a/docs/reference/applyAntsrTransform.html +++ b/docs/reference/applyAntsrTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/applyAntsrTransformToImage.html b/docs/reference/applyAntsrTransformToImage.html index 3a795fe8..72461381 100644 --- a/docs/reference/applyAntsrTransformToImage.html +++ b/docs/reference/applyAntsrTransformToImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/applyAntsrTransformToPoint.html b/docs/reference/applyAntsrTransformToPoint.html index 34e42fdd..8b5482e4 100644 --- a/docs/reference/applyAntsrTransformToPoint.html +++ b/docs/reference/applyAntsrTransformToPoint.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/applyAntsrTransformToVector.html b/docs/reference/applyAntsrTransformToVector.html index f0c1b0e3..0527c35e 100644 --- a/docs/reference/applyAntsrTransformToVector.html +++ b/docs/reference/applyAntsrTransformToVector.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/apply_simlr_matrices.html b/docs/reference/apply_simlr_matrices.html index 3283121e..58a8b0c8 100644 --- a/docs/reference/apply_simlr_matrices.html +++ b/docs/reference/apply_simlr_matrices.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/as.antsImage.html b/docs/reference/as.antsImage.html index fbf7f18d..cf0cb6f8 100644 --- a/docs/reference/as.antsImage.html +++ b/docs/reference/as.antsImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/as.antsMatrix.html b/docs/reference/as.antsMatrix.html index e81a85f6..afaf6ec7 100644 --- a/docs/reference/as.antsMatrix.html +++ b/docs/reference/as.antsMatrix.html @@ -32,7 +32,7 @@ @@ -89,7 +89,7 @@

Examples

#> [1] "float" #> #> Slot "pointer": -#> <pointer: 0x600000b45ec0> +#> <pointer: 0x6000039c5100> #> mat <- matrix(rnorm(10), nrow = 2) df <- as.data.frame(mat) @@ -99,7 +99,7 @@

Examples

#> [1] "float" #> #> Slot "pointer": -#> <pointer: 0x600000b45800> +#> <pointer: 0x6000039c5400> #> as.antsMatrix(as.list(df)) #> An object of class "antsMatrix" @@ -107,7 +107,7 @@

Examples

#> [1] "float" #> #> Slot "pointer": -#> <pointer: 0x600000b46040> +#> <pointer: 0x6000039c54c0> #> diff --git a/docs/reference/as.array.html b/docs/reference/as.array.html index b2da1aa0..cb6665a6 100644 --- a/docs/reference/as.array.html +++ b/docs/reference/as.array.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/aslAveraging.html b/docs/reference/aslAveraging.html index 9a5dc0c9..cafc63c7 100644 --- a/docs/reference/aslAveraging.html +++ b/docs/reference/aslAveraging.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/aslCensoring.html b/docs/reference/aslCensoring.html index eec3ff10..b83742db 100644 --- a/docs/reference/aslCensoring.html +++ b/docs/reference/aslCensoring.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/aslDenoiseR.html b/docs/reference/aslDenoiseR.html index a39e18b3..52448749 100644 --- a/docs/reference/aslDenoiseR.html +++ b/docs/reference/aslDenoiseR.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/aslPerfusion.html b/docs/reference/aslPerfusion.html index fe5a70b5..fe15b59b 100644 --- a/docs/reference/aslPerfusion.html +++ b/docs/reference/aslPerfusion.html @@ -40,7 +40,7 @@ diff --git a/docs/reference/atropos.html b/docs/reference/atropos.html index 1ee2c401..b83ae13b 100644 --- a/docs/reference/atropos.html +++ b/docs/reference/atropos.html @@ -38,7 +38,7 @@ diff --git a/docs/reference/basicInPaint.html b/docs/reference/basicInPaint.html index 89c5ae05..74fa5fe6 100644 --- a/docs/reference/basicInPaint.html +++ b/docs/reference/basicInPaint.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/bayesianCBF.html b/docs/reference/bayesianCBF.html index 6d646cb5..553fe871 100644 --- a/docs/reference/bayesianCBF.html +++ b/docs/reference/bayesianCBF.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/bayesianlm.html b/docs/reference/bayesianlm.html index a4e05dad..d4b247d0 100644 --- a/docs/reference/bayesianlm.html +++ b/docs/reference/bayesianlm.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/bigLMStats.html b/docs/reference/bigLMStats.html index 0b207405..09ccdad1 100644 --- a/docs/reference/bigLMStats.html +++ b/docs/reference/bigLMStats.html @@ -40,7 +40,7 @@ diff --git a/docs/reference/blockStimulus.html b/docs/reference/blockStimulus.html index 28ae415b..414f9c10 100644 --- a/docs/reference/blockStimulus.html +++ b/docs/reference/blockStimulus.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/bloodPerfusionSVD.html b/docs/reference/bloodPerfusionSVD.html index 9ee5809e..25e2985a 100644 --- a/docs/reference/bloodPerfusionSVD.html +++ b/docs/reference/bloodPerfusionSVD.html @@ -37,7 +37,7 @@ diff --git a/docs/reference/bold_correlation_matrix.html b/docs/reference/bold_correlation_matrix.html index 43f28419..150bde75 100644 --- a/docs/reference/bold_correlation_matrix.html +++ b/docs/reference/bold_correlation_matrix.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/boxplot.antsImage.html b/docs/reference/boxplot.antsImage.html index f998d297..136067f6 100644 --- a/docs/reference/boxplot.antsImage.html +++ b/docs/reference/boxplot.antsImage.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/brackets.html b/docs/reference/brackets.html index 10e2d061..a520eda9 100644 --- a/docs/reference/brackets.html +++ b/docs/reference/brackets.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/buildTemplate.html b/docs/reference/buildTemplate.html index 21982bd3..861a11ec 100644 --- a/docs/reference/buildTemplate.html +++ b/docs/reference/buildTemplate.html @@ -35,7 +35,7 @@ @@ -142,7 +142,7 @@

Examples

#> ================================================================================ #> Averaging warped composed transforms #> ================================================================================ -#> Blending template image2.63243993823232 +#> Blending template image2.52680086332545 diff --git a/docs/reference/check_ants-methods.html b/docs/reference/check_ants-methods.html index 4d6058a5..ee82430e 100644 --- a/docs/reference/check_ants-methods.html +++ b/docs/reference/check_ants-methods.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/clusterTimeSeries.html b/docs/reference/clusterTimeSeries.html index ecb5abdf..7cecefdc 100644 --- a/docs/reference/clusterTimeSeries.html +++ b/docs/reference/clusterTimeSeries.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/coerce_mask.html b/docs/reference/coerce_mask.html index af985294..d8608647 100644 --- a/docs/reference/coerce_mask.html +++ b/docs/reference/coerce_mask.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/combineNuisancePredictors.html b/docs/reference/combineNuisancePredictors.html index 65089328..04bfb71b 100644 --- a/docs/reference/combineNuisancePredictors.html +++ b/docs/reference/combineNuisancePredictors.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/compcor.html b/docs/reference/compcor.html index 100bb046..dacaedbf 100644 --- a/docs/reference/compcor.html +++ b/docs/reference/compcor.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/composeAntsrTransforms.html b/docs/reference/composeAntsrTransforms.html index 57ec9522..74a9d912 100644 --- a/docs/reference/composeAntsrTransforms.html +++ b/docs/reference/composeAntsrTransforms.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/composeDisplacementFields.html b/docs/reference/composeDisplacementFields.html index 4f328656..9dcd284f 100644 --- a/docs/reference/composeDisplacementFields.html +++ b/docs/reference/composeDisplacementFields.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/composeTransformsToField.html b/docs/reference/composeTransformsToField.html index 0c24a41d..db1c5c44 100644 --- a/docs/reference/composeTransformsToField.html +++ b/docs/reference/composeTransformsToField.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/computeDVARS.html b/docs/reference/computeDVARS.html index 39306f36..30a8c6ae 100644 --- a/docs/reference/computeDVARS.html +++ b/docs/reference/computeDVARS.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/computeDVARSspatialMap.html b/docs/reference/computeDVARSspatialMap.html index 123261d7..edd7cda3 100644 --- a/docs/reference/computeDVARSspatialMap.html +++ b/docs/reference/computeDVARSspatialMap.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/convolveImage.html b/docs/reference/convolveImage.html index 975f9303..ed5ee484 100644 --- a/docs/reference/convolveImage.html +++ b/docs/reference/convolveImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/corw.html b/docs/reference/corw.html index 04488984..135c4493 100644 --- a/docs/reference/corw.html +++ b/docs/reference/corw.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/createAntsrTransform.html b/docs/reference/createAntsrTransform.html index 49302a8a..f31b9ee2 100644 --- a/docs/reference/createAntsrTransform.html +++ b/docs/reference/createAntsrTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/createJacobianDeterminantImage.html b/docs/reference/createJacobianDeterminantImage.html index 680507d8..cc61e308 100644 --- a/docs/reference/createJacobianDeterminantImage.html +++ b/docs/reference/createJacobianDeterminantImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/createWarpedGrid.html b/docs/reference/createWarpedGrid.html index 6041e3f8..fb316ff6 100644 --- a/docs/reference/createWarpedGrid.html +++ b/docs/reference/createWarpedGrid.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/cropImage.html b/docs/reference/cropImage.html index 7fdfad03..5b0873b1 100644 --- a/docs/reference/cropImage.html +++ b/docs/reference/cropImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/cropIndices.html b/docs/reference/cropIndices.html index b6961f42..5dbba756 100644 --- a/docs/reference/cropIndices.html +++ b/docs/reference/cropIndices.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/crossvalidatedR2.html b/docs/reference/crossvalidatedR2.html index 86810f46..c5df467a 100644 --- a/docs/reference/crossvalidatedR2.html +++ b/docs/reference/crossvalidatedR2.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/cut.antsImage.html b/docs/reference/cut.antsImage.html index 555d48dd..3bd2d196 100644 --- a/docs/reference/cut.antsImage.html +++ b/docs/reference/cut.antsImage.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/cvEigenanatomy.html b/docs/reference/cvEigenanatomy.html index 6ee49016..29f5dc84 100644 --- a/docs/reference/cvEigenanatomy.html +++ b/docs/reference/cvEigenanatomy.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/deconvolutionSVD.html b/docs/reference/deconvolutionSVD.html index 53a4ff84..5da0872a 100644 --- a/docs/reference/deconvolutionSVD.html +++ b/docs/reference/deconvolutionSVD.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/decropImage.html b/docs/reference/decropImage.html index 667db86f..c12ebe8c 100644 --- a/docs/reference/decropImage.html +++ b/docs/reference/decropImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/denoiseImage.html b/docs/reference/denoiseImage.html index fc9863a8..bff85d61 100644 --- a/docs/reference/denoiseImage.html +++ b/docs/reference/denoiseImage.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/density.antsImage.html b/docs/reference/density.antsImage.html index 48096b2d..f0463517 100644 --- a/docs/reference/density.antsImage.html +++ b/docs/reference/density.antsImage.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/displacementFieldFromAntsrTransform.html b/docs/reference/displacementFieldFromAntsrTransform.html index 94a71cf6..4745422e 100644 --- a/docs/reference/displacementFieldFromAntsrTransform.html +++ b/docs/reference/displacementFieldFromAntsrTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/divide_by_column_sum.html b/docs/reference/divide_by_column_sum.html index 81a84d50..98511dda 100644 --- a/docs/reference/divide_by_column_sum.html +++ b/docs/reference/divide_by_column_sum.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/eanatDef.html b/docs/reference/eanatDef.html index 150d45a5..6bdea6ce 100644 --- a/docs/reference/eanatDef.html +++ b/docs/reference/eanatDef.html @@ -37,7 +37,7 @@ diff --git a/docs/reference/eanatSelect.html b/docs/reference/eanatSelect.html index 643f45f2..48d57a2e 100644 --- a/docs/reference/eanatSelect.html +++ b/docs/reference/eanatSelect.html @@ -38,7 +38,7 @@ diff --git a/docs/reference/eigSeg.html b/docs/reference/eigSeg.html index 24618ed9..6c2fb773 100644 --- a/docs/reference/eigSeg.html +++ b/docs/reference/eigSeg.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/error_not_antsImage.html b/docs/reference/error_not_antsImage.html index e9091326..86d61514 100644 --- a/docs/reference/error_not_antsImage.html +++ b/docs/reference/error_not_antsImage.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/estSmooth.html b/docs/reference/estSmooth.html index 3fe8d4a5..feef5e95 100644 --- a/docs/reference/estSmooth.html +++ b/docs/reference/estSmooth.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/euler.html b/docs/reference/euler.html index 3095da71..5ab7fc97 100644 --- a/docs/reference/euler.html +++ b/docs/reference/euler.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/exemplarInpainting.html b/docs/reference/exemplarInpainting.html index 88d25c61..3d526968 100644 --- a/docs/reference/exemplarInpainting.html +++ b/docs/reference/exemplarInpainting.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/extractSlice.html b/docs/reference/extractSlice.html index 5c5bd25f..6e1c3da4 100644 --- a/docs/reference/extractSlice.html +++ b/docs/reference/extractSlice.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/fMRINormalization.html b/docs/reference/fMRINormalization.html index 30a32f7a..da872ebc 100644 --- a/docs/reference/fMRINormalization.html +++ b/docs/reference/fMRINormalization.html @@ -40,7 +40,7 @@ diff --git a/docs/reference/fastMarchingExtension.html b/docs/reference/fastMarchingExtension.html index e491f202..3c442208 100644 --- a/docs/reference/fastMarchingExtension.html +++ b/docs/reference/fastMarchingExtension.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/filterfMRIforNetworkAnalysis.html b/docs/reference/filterfMRIforNetworkAnalysis.html index 14e2cddf..ef377f18 100644 --- a/docs/reference/filterfMRIforNetworkAnalysis.html +++ b/docs/reference/filterfMRIforNetworkAnalysis.html @@ -42,7 +42,7 @@ diff --git a/docs/reference/fitBsplineDisplacementField.html b/docs/reference/fitBsplineDisplacementField.html index bca2e6b5..2086af82 100644 --- a/docs/reference/fitBsplineDisplacementField.html +++ b/docs/reference/fitBsplineDisplacementField.html @@ -37,7 +37,7 @@ diff --git a/docs/reference/fitBsplineObjectToScatteredData.html b/docs/reference/fitBsplineObjectToScatteredData.html index d7044608..3e8f80fd 100644 --- a/docs/reference/fitBsplineObjectToScatteredData.html +++ b/docs/reference/fitBsplineObjectToScatteredData.html @@ -47,7 +47,7 @@ diff --git a/docs/reference/fitThinPlateSplineDisplacementField.html b/docs/reference/fitThinPlateSplineDisplacementField.html index b46424b9..9665a228 100644 --- a/docs/reference/fitThinPlateSplineDisplacementField.html +++ b/docs/reference/fitThinPlateSplineDisplacementField.html @@ -35,7 +35,7 @@ diff --git a/docs/reference/fitTimeVaryingTransformToPointSets.html b/docs/reference/fitTimeVaryingTransformToPointSets.html index 69e5d90a..8bb35f3c 100644 --- a/docs/reference/fitTimeVaryingTransformToPointSets.html +++ b/docs/reference/fitTimeVaryingTransformToPointSets.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/fitTransformToPairedPoints.html b/docs/reference/fitTransformToPairedPoints.html index a1c6c3bd..eb007078 100644 --- a/docs/reference/fitTransformToPairedPoints.html +++ b/docs/reference/fitTransformToPairedPoints.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/frequencyFilterfMRI.html b/docs/reference/frequencyFilterfMRI.html index 20e5c8cc..14c188b2 100644 --- a/docs/reference/frequencyFilterfMRI.html +++ b/docs/reference/frequencyFilterfMRI.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/fsl2antsrTransform.html b/docs/reference/fsl2antsrTransform.html index cb94fce2..917337ab 100644 --- a/docs/reference/fsl2antsrTransform.html +++ b/docs/reference/fsl2antsrTransform.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/functionalLungSegmentation.html b/docs/reference/functionalLungSegmentation.html index de8aff67..f2c9e369 100644 --- a/docs/reference/functionalLungSegmentation.html +++ b/docs/reference/functionalLungSegmentation.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/fuzzySpatialCMeansSegmentation.html b/docs/reference/fuzzySpatialCMeansSegmentation.html index 6252d40e..a05b7e63 100644 --- a/docs/reference/fuzzySpatialCMeansSegmentation.html +++ b/docs/reference/fuzzySpatialCMeansSegmentation.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/generateAifMaskImage.html b/docs/reference/generateAifMaskImage.html index 0a73f837..e00e66c6 100644 --- a/docs/reference/generateAifMaskImage.html +++ b/docs/reference/generateAifMaskImage.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/geoSeg.html b/docs/reference/geoSeg.html index e828614a..a3ede312 100644 --- a/docs/reference/geoSeg.html +++ b/docs/reference/geoSeg.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getANTsRData.html b/docs/reference/getANTsRData.html index d33d8f40..8e1983db 100644 --- a/docs/reference/getANTsRData.html +++ b/docs/reference/getANTsRData.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getASLNoisePredictors.html b/docs/reference/getASLNoisePredictors.html index 2f452691..4cd7b9a0 100644 --- a/docs/reference/getASLNoisePredictors.html +++ b/docs/reference/getASLNoisePredictors.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getAntsrTransformFixedParameters.html b/docs/reference/getAntsrTransformFixedParameters.html index 778a1fa7..d83d541b 100644 --- a/docs/reference/getAntsrTransformFixedParameters.html +++ b/docs/reference/getAntsrTransformFixedParameters.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getAntsrTransformParameters.html b/docs/reference/getAntsrTransformParameters.html index fe4b721c..eeb0d4f4 100644 --- a/docs/reference/getAntsrTransformParameters.html +++ b/docs/reference/getAntsrTransformParameters.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getAverageOfTimeSeries.html b/docs/reference/getAverageOfTimeSeries.html index ca88698d..08120d77 100644 --- a/docs/reference/getAverageOfTimeSeries.html +++ b/docs/reference/getAverageOfTimeSeries.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getCenterOfMass.html b/docs/reference/getCenterOfMass.html index ef936035..7dfa9b5d 100644 --- a/docs/reference/getCenterOfMass.html +++ b/docs/reference/getCenterOfMass.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/getCentroids.html b/docs/reference/getCentroids.html index c06e4876..35da074e 100644 --- a/docs/reference/getCentroids.html +++ b/docs/reference/getCentroids.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/getMask.html b/docs/reference/getMask.html index dfe3f745..7a026155 100644 --- a/docs/reference/getMask.html +++ b/docs/reference/getMask.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getMultiResFeatureMatrix.html b/docs/reference/getMultiResFeatureMatrix.html index 1ff7ac90..690daf95 100644 --- a/docs/reference/getMultiResFeatureMatrix.html +++ b/docs/reference/getMultiResFeatureMatrix.html @@ -42,7 +42,7 @@ diff --git a/docs/reference/getMultivariateTemplateCoordinates.html b/docs/reference/getMultivariateTemplateCoordinates.html index fabcafa5..f42daec6 100644 --- a/docs/reference/getMultivariateTemplateCoordinates.html +++ b/docs/reference/getMultivariateTemplateCoordinates.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/getNeighborhoodAtVoxel.html b/docs/reference/getNeighborhoodAtVoxel.html index c6a07166..1a19f867 100644 --- a/docs/reference/getNeighborhoodAtVoxel.html +++ b/docs/reference/getNeighborhoodAtVoxel.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getNeighborhoodInMask.html b/docs/reference/getNeighborhoodInMask.html index 1f29f08a..e7f085b8 100644 --- a/docs/reference/getNeighborhoodInMask.html +++ b/docs/reference/getNeighborhoodInMask.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/getPixels.html b/docs/reference/getPixels.html index d2673fa3..2feef7de 100644 --- a/docs/reference/getPixels.html +++ b/docs/reference/getPixels.html @@ -32,7 +32,7 @@ diff --git a/docs/reference/getTemplateCoordinates.html b/docs/reference/getTemplateCoordinates.html index a8eb4157..f958190c 100644 --- a/docs/reference/getTemplateCoordinates.html +++ b/docs/reference/getTemplateCoordinates.html @@ -33,7 +33,7 @@ diff --git a/docs/reference/getfMRInuisanceVariables.html b/docs/reference/getfMRInuisanceVariables.html index 9446d818..f17cd252 100644 --- a/docs/reference/getfMRInuisanceVariables.html +++ b/docs/reference/getfMRInuisanceVariables.html @@ -36,7 +36,7 @@ diff --git a/docs/reference/gradient_invariant_orthogonality_defect.html b/docs/reference/gradient_invariant_orthogonality_defect.html index be4cacc6..90f86314 100644 --- a/docs/reference/gradient_invariant_orthogonality_defect.html +++ b/docs/reference/gradient_invariant_orthogonality_defect.html @@ -34,7 +34,7 @@ diff --git a/docs/reference/gradient_invariant_orthogonality_salad.html b/docs/reference/gradient_invariant_orthogonality_salad.html index fe9e3985..9321c65c 100644 --- a/docs/reference/gradient_invariant_orthogonality_salad.html +++ b/docs/reference/gradient_invariant_orthogonality_salad.html @@ -34,7 +34,7 @@ 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    diff --git a/docs/reference/histogramEqualizeImage.html b/docs/reference/histogramEqualizeImage.html index 3c0ba455..85063850 100644 --- a/docs/reference/histogramEqualizeImage.html +++ b/docs/reference/histogramEqualizeImage.html @@ -32,7 +32,7 @@
      diff --git a/docs/reference/histogramMatchImage.html b/docs/reference/histogramMatchImage.html index c1dc34cd..480b3ca9 100644 --- a/docs/reference/histogramMatchImage.html +++ b/docs/reference/histogramMatchImage.html @@ -32,7 +32,7 @@
        diff --git a/docs/reference/histogramMatchImage2.html b/docs/reference/histogramMatchImage2.html index 4c6f75aa..0ee24944 100644 --- a/docs/reference/histogramMatchImage2.html +++ b/docs/reference/histogramMatchImage2.html @@ -32,7 +32,7 @@
          diff --git a/docs/reference/iBind.html b/docs/reference/iBind.html index 28f859b8..137b4ed0 100644 --- a/docs/reference/iBind.html +++ b/docs/reference/iBind.html @@ -32,7 +32,7 @@
            diff --git a/docs/reference/iMath.html b/docs/reference/iMath.html index d02ec7a7..19e678f7 100644 --- a/docs/reference/iMath.html +++ b/docs/reference/iMath.html @@ -34,7 +34,7 @@
              diff --git a/docs/reference/iMathOps.html b/docs/reference/iMathOps.html index f579df61..98365b1e 100644 --- a/docs/reference/iMathOps.html +++ b/docs/reference/iMathOps.html @@ -32,7 +32,7 @@
                diff --git a/docs/reference/icawhiten.html b/docs/reference/icawhiten.html index 1b2d27f9..98cf1769 100644 --- a/docs/reference/icawhiten.html +++ b/docs/reference/icawhiten.html @@ -32,7 +32,7 @@
                  diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index aa24cbb9..3960ec2d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -37,7 +37,7 @@
                    diff --git a/docs/reference/ilr.predict.html b/docs/reference/ilr.predict.html index 1e82bcc4..8f8d6194 100644 --- a/docs/reference/ilr.predict.html +++ b/docs/reference/ilr.predict.html @@ -32,7 +32,7 @@
                      diff --git a/docs/reference/image2ClusterImages.html b/docs/reference/image2ClusterImages.html index 580e1324..00e2808e 100644 --- a/docs/reference/image2ClusterImages.html +++ b/docs/reference/image2ClusterImages.html @@ -33,7 +33,7 @@
                        diff --git a/docs/reference/imageDomainToSpatialMatrix.html b/docs/reference/imageDomainToSpatialMatrix.html index 3f463886..c47e607e 100644 --- a/docs/reference/imageDomainToSpatialMatrix.html +++ b/docs/reference/imageDomainToSpatialMatrix.html @@ -33,7 +33,7 @@
                          diff --git a/docs/reference/imageFileNames2ImageList.html b/docs/reference/imageFileNames2ImageList.html index 108aefc9..4ed7080c 100644 --- a/docs/reference/imageFileNames2ImageList.html +++ b/docs/reference/imageFileNames2ImageList.html @@ -33,7 +33,7 @@
                            diff --git a/docs/reference/imageListToMatrix.html b/docs/reference/imageListToMatrix.html index 7a488de7..e8ffe9a8 100644 --- a/docs/reference/imageListToMatrix.html +++ b/docs/reference/imageListToMatrix.html @@ -32,7 +32,7 @@
                              diff --git a/docs/reference/imageSimilarity.html b/docs/reference/imageSimilarity.html index be582f5b..2b95be4e 100644 --- a/docs/reference/imageSimilarity.html +++ b/docs/reference/imageSimilarity.html @@ -32,7 +32,7 @@
                                diff --git a/docs/reference/imagesToMatrix.html b/docs/reference/imagesToMatrix.html index ea8f3841..48dd9904 100644 --- a/docs/reference/imagesToMatrix.html +++ b/docs/reference/imagesToMatrix.html @@ -33,7 +33,7 @@
                                  @@ -103,7 +103,7 @@

                                  Examples

                                  mask <- getMask(antsImageRead(imageList[1])) mat <- imagesToMatrix(imageList, mask) print(dim(mat)) -#> [1] 3 58 +#> [1] 3 18017 diff --git a/docs/reference/index.html b/docs/reference/index.html index 7b85ebd5..653b1abf 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -32,7 +32,7 @@
                                    @@ -271,6 +271,30 @@

                                    All functions antsVersions

                                    antsVersions

                                    + +

                                    antspymm_nuisance_names()

                                    + +

                                    return nuisance variable strings

                                    + +

                                    antspymm_predictors()

                                    + +

                                    Generate Predictors from ANTsPyMM Imaging Data

                                    + +

                                    antspymm_qc_names()

                                    + +

                                    Get Quality Control (QC) Metric Names

                                    + +

                                    antspymm_simlr()

                                    + +

                                    Perform SiMLR Analysis on Multimodal ANTsPyMM Data

                                    + +

                                    antspymm_simlr_update_residuals()

                                    + +

                                    Update Residuals for SiMLR

                                    + +

                                    antspymm_vartype()

                                    + +

                                    Determine the Variable Type Based on Its Name

                                    antsrGetPointerName()

                                    @@ -588,6 +612,10 @@

                                    All functions exemplarInpainting()

                                    Uses example images to inpaint or approximate an existing image.

                                    + +

                                    exploratory_visualization()

                                    + +

                                    Exploratory Clustering and Visualization

                                    extractSlice()

                                    @@ -709,6 +737,10 @@

                                    All functions getfMRInuisanceVariables()

                                    Extract generic fMRI nuisance variables for ASL or BOLD

                                    + +

                                    glm_impute()

                                    + +

                                    Impute missing data using GLM models

                                    gradient_invariant_orthogonality_defect()

                                    @@ -822,6 +854,14 @@

                                    All functions interleaveMatrixWithItself()

                                    Simple interleaveMatrixWithItself function.

                                    + +

                                    interpret_simlr_vector()

                                    + +

                                    Interpret SiMLR Vector

                                    + +

                                    interpret_simlr_vector2()

                                    + +

                                    Interpret SiMLR Vector

                                    invariant_orthogonality_defect()

                                    @@ -1074,6 +1114,10 @@

                                    All functions plotPrettyGraph()

                                    Simple plotPrettyGraph function saves to png.

                                    + +

                                    plot_features()

                                    + +

                                    Plot Features

                                    powers_areal_mni_itk

                                    @@ -1142,6 +1186,10 @@

                                    All functions readNormalizedPopulationData()

                                    Read normalized population from h5 file or directory

                                    + +

                                    read_simlr_data_frames()

                                    + +

                                    Read a list of data frames from disk with specific naming convention

                                    reflectImage()

                                    @@ -1242,6 +1290,10 @@

                                    All functions setAntsrTransformParameters()

                                    setAntsrTransformParameters

                                    + +

                                    shorten_pymm_names()

                                    + +

                                    shorter antspymm names

                                    simlr()

                                    @@ -1262,6 +1314,10 @@

                                    All functions simlrU()

                                    Compute the low-dimensional u matrix for simlr

                                    + +

                                    simlr_impute()

                                    + +

                                    Impute missing SiMLR data in a specified column based on other columns

                                    simlr_path_models()

                                    @@ -1423,6 +1479,10 @@

                                    All functions visualize_lowrank_relationships()

                                    Visualize Low-Rank Relationships

                                    + +

                                    visualize_permutation_test()

                                    + +

                                    Visualize Permutation Test Results

                                    vwnrfs()

                                    @@ -1451,6 +1511,10 @@

                                    All functions writeNormalizedPopulationData()

                                    Save normalized population data to a directory or h5 file

                                    + +

                                    write_simlr_data_frames()

                                    + +

                                    Write a list of data frames to disk with specific naming convention

                                    diff --git a/docs/reference/initializeSimlr.html b/docs/reference/initializeSimlr.html index 6d613e22..96038282 100644 --- a/docs/reference/initializeSimlr.html +++ b/docs/reference/initializeSimlr.html @@ -36,7 +36,7 @@
                                      diff --git a/docs/reference/int_antsProcessArguments.html b/docs/reference/int_antsProcessArguments.html index 4e7b54f0..87e1d2ac 100644 --- a/docs/reference/int_antsProcessArguments.html +++ b/docs/reference/int_antsProcessArguments.html @@ -32,7 +32,7 @@
                                        diff --git a/docs/reference/integrateVectorField.html b/docs/reference/integrateVectorField.html index 864c1192..8d3b0b8f 100644 --- a/docs/reference/integrateVectorField.html +++ b/docs/reference/integrateVectorField.html @@ -32,7 +32,7 @@
                                          diff --git a/docs/reference/integrateVelocityField.html b/docs/reference/integrateVelocityField.html index 6ad2efb8..70a0656e 100644 --- a/docs/reference/integrateVelocityField.html +++ b/docs/reference/integrateVelocityField.html @@ -32,7 +32,7 @@
                                            diff --git a/docs/reference/interleaveMatrixWithItself.html b/docs/reference/interleaveMatrixWithItself.html index be3ef3fa..0ff8f1cd 100644 --- a/docs/reference/interleaveMatrixWithItself.html +++ b/docs/reference/interleaveMatrixWithItself.html @@ -33,7 +33,7 @@
                                              diff --git a/docs/reference/invariant_orthogonality_defect.html b/docs/reference/invariant_orthogonality_defect.html index 16f07ae4..f06cae30 100644 --- a/docs/reference/invariant_orthogonality_defect.html +++ b/docs/reference/invariant_orthogonality_defect.html @@ -32,7 +32,7 @@
                                                diff --git a/docs/reference/invertAntsrTransform.html b/docs/reference/invertAntsrTransform.html index f8fc42f7..530722e4 100644 --- a/docs/reference/invertAntsrTransform.html +++ b/docs/reference/invertAntsrTransform.html @@ -32,7 +32,7 @@
                                                  diff --git a/docs/reference/invertDisplacementField.html b/docs/reference/invertDisplacementField.html index 91e0e694..9cd8c33c 100644 --- a/docs/reference/invertDisplacementField.html +++ b/docs/reference/invertDisplacementField.html @@ -32,7 +32,7 @@
                                                    diff --git a/docs/reference/is.antsImage.html b/docs/reference/is.antsImage.html index b6ee40ca..53e3d83f 100644 --- a/docs/reference/is.antsImage.html +++ b/docs/reference/is.antsImage.html @@ -32,7 +32,7 @@
                                                      diff --git a/docs/reference/jlfProp.html b/docs/reference/jlfProp.html index 5e983606..13112049 100644 --- a/docs/reference/jlfProp.html +++ b/docs/reference/jlfProp.html @@ -33,7 +33,7 @@
                                                        diff --git a/docs/reference/joinEigenanatomy.html b/docs/reference/joinEigenanatomy.html index 52c08b2d..d70684d2 100644 --- a/docs/reference/joinEigenanatomy.html +++ b/docs/reference/joinEigenanatomy.html @@ -33,7 +33,7 @@
                                                          diff --git a/docs/reference/jointLabelFusion.html b/docs/reference/jointLabelFusion.html index 1ba98fb1..744d1c74 100644 --- a/docs/reference/jointLabelFusion.html +++ b/docs/reference/jointLabelFusion.html @@ -41,7 +41,7 @@
                                                            diff --git a/docs/reference/jointSmoothMatrixReconstruction.html b/docs/reference/jointSmoothMatrixReconstruction.html index bbd05e2d..e988d7ec 100644 --- a/docs/reference/jointSmoothMatrixReconstruction.html +++ b/docs/reference/jointSmoothMatrixReconstruction.html @@ -34,7 +34,7 @@
                                                              diff --git a/docs/reference/kellyKapowski.html b/docs/reference/kellyKapowski.html index 29349417..29a07918 100644 --- a/docs/reference/kellyKapowski.html +++ b/docs/reference/kellyKapowski.html @@ -33,7 +33,7 @@
                                                                diff --git a/docs/reference/kmeansSegmentation.html b/docs/reference/kmeansSegmentation.html index 03405c42..626415db 100644 --- a/docs/reference/kmeansSegmentation.html +++ b/docs/reference/kmeansSegmentation.html @@ -32,7 +32,7 @@
                                                                  @@ -124,9 +124,9 @@

                                                                  Examples

                                                                  #> arr2 #> arr1 0 1 2 3 #> 0 47118 0 0 0 -#> 1 0 2383 0 0 -#> 2 0 0 7355 1 -#> 3 0 0 4 8675 +#> 1 0 2380 2 0 +#> 2 0 4 7350 7 +#> 3 0 0 3 8672 identical(arr1, arr2) #> [1] FALSE seg <- kmeansSegmentation(orig, 3, use_random_seed = FALSE) diff --git a/docs/reference/knnSmoothImage.html b/docs/reference/knnSmoothImage.html index 6eae26c4..b29c2fa0 100644 --- a/docs/reference/knnSmoothImage.html +++ b/docs/reference/knnSmoothImage.html @@ -34,7 +34,7 @@
                                                                    diff --git a/docs/reference/knnSmoothingMatrix.html b/docs/reference/knnSmoothingMatrix.html index b0604a92..28fa71e3 100644 --- a/docs/reference/knnSmoothingMatrix.html +++ b/docs/reference/knnSmoothingMatrix.html @@ -32,7 +32,7 @@
                                                                      diff --git a/docs/reference/labelClusters.html b/docs/reference/labelClusters.html index 4b45d41c..577970a9 100644 --- a/docs/reference/labelClusters.html +++ b/docs/reference/labelClusters.html @@ -33,7 +33,7 @@
                                                                        diff --git a/docs/reference/labelGeometryMeasures.html b/docs/reference/labelGeometryMeasures.html index 0192a728..04038f71 100644 --- a/docs/reference/labelGeometryMeasures.html +++ b/docs/reference/labelGeometryMeasures.html @@ -32,7 +32,7 @@
                                                                          diff --git a/docs/reference/labelImageCentroids.html b/docs/reference/labelImageCentroids.html index 06dbb6a3..977ad7c7 100644 --- a/docs/reference/labelImageCentroids.html +++ b/docs/reference/labelImageCentroids.html @@ -32,7 +32,7 @@
                                                                            diff --git a/docs/reference/labelOverlapMeasures.html b/docs/reference/labelOverlapMeasures.html index f4f00aab..f980ae13 100644 --- a/docs/reference/labelOverlapMeasures.html +++ b/docs/reference/labelOverlapMeasures.html @@ -33,7 +33,7 @@
                                                                              diff --git a/docs/reference/labelStats.html b/docs/reference/labelStats.html index 192b0471..6f7eaac4 100644 --- a/docs/reference/labelStats.html +++ b/docs/reference/labelStats.html @@ -32,7 +32,7 @@
                                                                                @@ -85,14 +85,14 @@

                                                                                Examples

                                                                                labelStats(img, segs1$segmentation) #> LabelValue Mean Min Max Variance Count Volume Mass x #> 4 0 0.1475076 0 163 11.53692 2949 47184 0 0.0000 -#> 3 1 73.7428571 0 125 1535.97657 140 2240 10324 131.2857 +#> 1 1 73.7428571 0 125 1535.97657 140 2240 10324 131.2857 #> 2 2 166.1126126 127 191 259.86088 444 7104 73754 125.6937 -#> 1 3 216.2557726 191 253 221.33660 563 9008 121752 124.4618 +#> 3 3 216.2557726 191 253 221.33660 563 9008 121752 124.4618 #> y z t #> 4 0.0000 NA NA -#> 3 128.9714 NA NA +#> 1 128.9714 NA NA #> 2 126.0541 NA NA -#> 1 131.7300 NA NA +#> 3 131.7300 NA NA testthat::expect_error(labelStats(img, as.array(segs1$segmentation))) testthat::expect_error(labelStats(img, as.array(segs1$segmentation))) sub_seg <- segs1$segmentation diff --git a/docs/reference/labels2matrix.html b/docs/reference/labels2matrix.html index f6f08f83..06ac2693 100644 --- a/docs/reference/labels2matrix.html +++ b/docs/reference/labels2matrix.html @@ -35,7 +35,7 @@
                                                                                  diff --git a/docs/reference/lappend.html b/docs/reference/lappend.html index 969d7350..ee077527 100644 --- a/docs/reference/lappend.html +++ b/docs/reference/lappend.html @@ -32,7 +32,7 @@
                                                                                    diff --git a/docs/reference/load.ANTsR.html b/docs/reference/load.ANTsR.html index f203caf9..9049ab09 100644 --- a/docs/reference/load.ANTsR.html +++ b/docs/reference/load.ANTsR.html @@ -34,7 +34,7 @@
                                                                                      diff --git a/docs/reference/localGyrificationIndex.html b/docs/reference/localGyrificationIndex.html index 804d89a0..53a9789f 100644 --- a/docs/reference/localGyrificationIndex.html +++ b/docs/reference/localGyrificationIndex.html @@ -36,7 +36,7 @@
                                                                                        diff --git a/docs/reference/localJointLabelFusion.html b/docs/reference/localJointLabelFusion.html index 211b5849..d108f09c 100644 --- a/docs/reference/localJointLabelFusion.html +++ b/docs/reference/localJointLabelFusion.html @@ -37,7 +37,7 @@
                                                                                          diff --git a/docs/reference/lowrankRowMatrix.html b/docs/reference/lowrankRowMatrix.html index 514c1dec..096a5396 100644 --- a/docs/reference/lowrankRowMatrix.html +++ b/docs/reference/lowrankRowMatrix.html @@ -32,7 +32,7 @@
                                                                                            diff --git a/docs/reference/make3ViewPNG.html b/docs/reference/make3ViewPNG.html index 3070a6ec..d5e42f4f 100644 --- a/docs/reference/make3ViewPNG.html +++ b/docs/reference/make3ViewPNG.html @@ -35,7 +35,7 @@
                                                                                              diff --git a/docs/reference/makeGraph.html b/docs/reference/makeGraph.html index 9dc4b7d6..28d8c42c 100644 --- a/docs/reference/makeGraph.html +++ b/docs/reference/makeGraph.html @@ -34,7 +34,7 @@
                                                                                                diff --git a/docs/reference/makeImage.html b/docs/reference/makeImage.html index f9d8cf9e..1f15dc64 100644 --- a/docs/reference/makeImage.html +++ b/docs/reference/makeImage.html @@ -32,7 +32,7 @@
                                                                                                  diff --git a/docs/reference/makePointsImage.html b/docs/reference/makePointsImage.html index 22317e79..ec3df43e 100644 --- a/docs/reference/makePointsImage.html +++ b/docs/reference/makePointsImage.html @@ -35,7 +35,7 @@
                                                                                                    diff --git a/docs/reference/makePowersPointsImage.html b/docs/reference/makePowersPointsImage.html index a208abc6..f92dca85 100644 --- a/docs/reference/makePowersPointsImage.html +++ b/docs/reference/makePowersPointsImage.html @@ -32,7 +32,7 @@
                                                                                                      diff --git a/docs/reference/maskImage.html b/docs/reference/maskImage.html index 34397b63..0a044f38 100644 --- a/docs/reference/maskImage.html +++ b/docs/reference/maskImage.html @@ -33,7 +33,7 @@
                                                                                                        diff --git a/docs/reference/mask_values.html b/docs/reference/mask_values.html index 62f83d63..588063fe 100644 --- a/docs/reference/mask_values.html +++ b/docs/reference/mask_values.html @@ -32,7 +32,7 @@
                                                                                                          diff --git a/docs/reference/matrix2timeseries.html b/docs/reference/matrix2timeseries.html index 033b252a..a1071c4e 100644 --- a/docs/reference/matrix2timeseries.html +++ b/docs/reference/matrix2timeseries.html @@ -32,7 +32,7 @@
                                                                                                            diff --git a/docs/reference/matrixToImages.html b/docs/reference/matrixToImages.html index b811e4e3..784469e3 100644 --- a/docs/reference/matrixToImages.html +++ b/docs/reference/matrixToImages.html @@ -32,7 +32,7 @@
                                                                                                              diff --git a/docs/reference/mean.html b/docs/reference/mean.html index d101654b..898173d5 100644 --- a/docs/reference/mean.html +++ b/docs/reference/mean.html @@ -32,7 +32,7 @@
                                                                                                                diff --git a/docs/reference/median.html b/docs/reference/median.html index b37dae35..df699a03 100644 --- a/docs/reference/median.html +++ b/docs/reference/median.html @@ -32,7 +32,7 @@
                                                                                                                  diff --git a/docs/reference/mergeChannels.html b/docs/reference/mergeChannels.html index d34e68f9..5b29d1cf 100644 --- a/docs/reference/mergeChannels.html +++ b/docs/reference/mergeChannels.html @@ -32,7 +32,7 @@
                                                                                                                    diff --git a/docs/reference/mergeListToNDImage.html b/docs/reference/mergeListToNDImage.html index fb6414ad..fab2979f 100644 --- a/docs/reference/mergeListToNDImage.html +++ b/docs/reference/mergeListToNDImage.html @@ -33,7 +33,7 @@
                                                                                                                      diff --git a/docs/reference/mild.html b/docs/reference/mild.html index cc49aa10..a5b43af8 100644 --- a/docs/reference/mild.html +++ b/docs/reference/mild.html @@ -36,7 +36,7 @@
                                                                                                                        diff --git a/docs/reference/milr.html b/docs/reference/milr.html index bb58423b..42d6abf1 100644 --- a/docs/reference/milr.html +++ b/docs/reference/milr.html @@ -39,7 +39,7 @@
                                                                                                                          diff --git a/docs/reference/milr.predict.html b/docs/reference/milr.predict.html index 72e102ff..11c37353 100644 --- a/docs/reference/milr.predict.html +++ b/docs/reference/milr.predict.html @@ -35,7 +35,7 @@
                                                                                                                            diff --git a/docs/reference/mni2tal.html b/docs/reference/mni2tal.html index 3a3ff2ce..85dfea6f 100644 --- a/docs/reference/mni2tal.html +++ b/docs/reference/mni2tal.html @@ -32,7 +32,7 @@
                                                                                                                              diff --git a/docs/reference/morphology.html b/docs/reference/morphology.html index 12208e17..09002bfe 100644 --- a/docs/reference/morphology.html +++ b/docs/reference/morphology.html @@ -32,7 +32,7 @@
                                                                                                                                diff --git a/docs/reference/motion_correction.html b/docs/reference/motion_correction.html index 8928ab81..158a055c 100644 --- a/docs/reference/motion_correction.html +++ b/docs/reference/motion_correction.html @@ -32,7 +32,7 @@
                                                                                                                                  diff --git a/docs/reference/mrvnrfs.html b/docs/reference/mrvnrfs.html index 494fbac6..eb230100 100644 --- a/docs/reference/mrvnrfs.html +++ b/docs/reference/mrvnrfs.html @@ -33,7 +33,7 @@
                                                                                                                                    diff --git a/docs/reference/mrvnrfs.predict.html b/docs/reference/mrvnrfs.predict.html index 010319f8..52b8f06b 100644 --- a/docs/reference/mrvnrfs.predict.html +++ b/docs/reference/mrvnrfs.predict.html @@ -33,7 +33,7 @@
                                                                                                                                      diff --git a/docs/reference/multiLabelMorphology.html b/docs/reference/multiLabelMorphology.html index b8a5a0e1..7d8c80ee 100644 --- a/docs/reference/multiLabelMorphology.html +++ b/docs/reference/multiLabelMorphology.html @@ -33,7 +33,7 @@
                                                                                                                                        @@ -124,12 +124,12 @@

                                                                                                                                        Examples

                                                                                                                                        labelStats(labelsDilated, labels) #> LabelValue Mean Min Max Variance Count Volume Mass x y #> 3 0 0.01395981 0 2 0.02578888 64041 64041 0 0.0000 0.0000 -#> 2 1 2.00000000 2 2 0.00000000 216 216 432 149.5185 156.9815 -#> 1 2 2.00000000 2 2 0.00000000 1279 1279 2558 124.5676 130.9805 +#> 1 1 2.00000000 2 2 0.00000000 216 216 432 149.5185 156.9815 +#> 2 2 2.00000000 2 2 0.00000000 1279 1279 2558 124.5676 130.9805 #> z t #> 3 NA NA -#> 2 NA NA #> 1 NA NA +#> 2 NA NA diff --git a/docs/reference/multiResRandomForestRegression.html b/docs/reference/multiResRandomForestRegression.html index a77e7994..cbb2c179 100644 --- a/docs/reference/multiResRandomForestRegression.html +++ b/docs/reference/multiResRandomForestRegression.html @@ -36,7 +36,7 @@
                                                                                                                                          diff --git a/docs/reference/multichannelPCA.html b/docs/reference/multichannelPCA.html index 9acc24a7..466ea3d6 100644 --- a/docs/reference/multichannelPCA.html +++ b/docs/reference/multichannelPCA.html @@ -34,7 +34,7 @@
                                                                                                                                            diff --git a/docs/reference/multichannelToVector.html b/docs/reference/multichannelToVector.html index a317581f..1af3b94c 100644 --- a/docs/reference/multichannelToVector.html +++ b/docs/reference/multichannelToVector.html @@ -33,7 +33,7 @@
                                                                                                                                              diff --git a/docs/reference/multiscaleSVD.html b/docs/reference/multiscaleSVD.html index 1354a69b..b1879388 100644 --- a/docs/reference/multiscaleSVD.html +++ b/docs/reference/multiscaleSVD.html @@ -42,7 +42,7 @@
                                                                                                                                                diff --git a/docs/reference/n3BiasFieldCorrection.html b/docs/reference/n3BiasFieldCorrection.html index f42858cd..03f0fa47 100644 --- a/docs/reference/n3BiasFieldCorrection.html +++ b/docs/reference/n3BiasFieldCorrection.html @@ -32,7 +32,7 @@
                                                                                                                                                  diff --git a/docs/reference/n3BiasFieldCorrection2.html b/docs/reference/n3BiasFieldCorrection2.html index 1c1ded78..540fed64 100644 --- a/docs/reference/n3BiasFieldCorrection2.html +++ b/docs/reference/n3BiasFieldCorrection2.html @@ -32,7 +32,7 @@
                                                                                                                                                    @@ -146,21 +146,21 @@

                                                                                                                                                    Examples

                                                                                                                                                    rm(img) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3849724 205.6 5667982 302.8 NA 5667982 302.8 -#> Vcells 6353050 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3860875 206.2 6764756 361.3 NA 5603964 299.3 +#> Vcells 6375662 48.7 20537019 156.7 102400 20536927 156.7 rm(n3img) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3849433 205.6 5667982 302.8 NA 5667982 302.8 -#> Vcells 6352595 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3860509 206.2 6764756 361.3 NA 5603964 299.3 +#> Vcells 6375082 48.7 20537019 156.7 102400 20536927 156.7 fname <- getANTsRData("r16") in_img <- antsImageRead(fname) n3 <- n3BiasFieldCorrection2(in_img) rm(n3) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3849512 205.6 5667982 302.8 NA 5667982 302.8 -#> Vcells 6352714 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3860588 206.2 6764756 361.3 NA 5603964 299.3 +#> Vcells 6375201 48.7 20537019 156.7 102400 20536927 156.7 mask <- in_img > 0 mask2 <- antsImageClone(mask, out_pixeltype = "float") # fails diff --git a/docs/reference/n4BiasFieldCorrection.html b/docs/reference/n4BiasFieldCorrection.html index dfa793a1..c1bd5e37 100644 --- a/docs/reference/n4BiasFieldCorrection.html +++ b/docs/reference/n4BiasFieldCorrection.html @@ -32,7 +32,7 @@
                                                                                                                                                      @@ -142,21 +142,21 @@

                                                                                                                                                      Examples

                                                                                                                                                      rm(img) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3850028 205.7 5667982 302.8 NA 5667982 302.8 -#> Vcells 6353654 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3861110 206.3 6764756 361.3 NA 5603964 299.3 +#> Vcells 6376151 48.7 20537019 156.7 102400 20536927 156.7 rm(n4img) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3849467 205.6 5667982 302.8 NA 5667982 302.8 -#> Vcells 6352749 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3860543 206.2 6764756 361.3 NA 5603964 299.3 +#> Vcells 6375236 48.7 20537019 156.7 102400 20536927 156.7 fname <- getANTsRData("r16") in_img <- antsImageRead(fname) n4 <- n4BiasFieldCorrection(in_img) rm(n4) gc() #> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) -#> Ncells 3849546 205.6 5667982 302.8 NA 5667982 302.8 -#> Vcells 6352868 48.5 20521000 156.6 102400 20520992 156.6 +#> Ncells 3860622 206.2 6764756 361.3 NA 5603964 299.3 +#> Vcells 6375355 48.7 20537019 156.7 102400 20536927 156.7 mask <- in_img > 0 mask2 <- antsImageClone(mask, out_pixeltype = "float") # fails diff --git a/docs/reference/networkEiganat.html b/docs/reference/networkEiganat.html index 77e29814..4fbe1569 100644 --- a/docs/reference/networkEiganat.html +++ b/docs/reference/networkEiganat.html @@ -33,7 +33,7 @@
                                                                                                                                                        diff --git a/docs/reference/orthogonalizeAndQSparsify.html b/docs/reference/orthogonalizeAndQSparsify.html index 8890bd8a..dc28a827 100644 --- a/docs/reference/orthogonalizeAndQSparsify.html +++ b/docs/reference/orthogonalizeAndQSparsify.html @@ -32,7 +32,7 @@
                                                                                                                                                          diff --git a/docs/reference/orthogonalizeAndQSparsifyOld.html b/docs/reference/orthogonalizeAndQSparsifyOld.html index 8d7a4bf5..df144dd8 100644 --- a/docs/reference/orthogonalizeAndQSparsifyOld.html +++ b/docs/reference/orthogonalizeAndQSparsifyOld.html @@ -32,7 +32,7 @@
                                                                                                                                                            diff --git a/docs/reference/pairwiseImageDistanceMatrix.html b/docs/reference/pairwiseImageDistanceMatrix.html index 5c7ad7d2..c6cc6d67 100644 --- a/docs/reference/pairwiseImageDistanceMatrix.html +++ b/docs/reference/pairwiseImageDistanceMatrix.html @@ -37,7 +37,7 @@
                                                                                                                                                              diff --git a/docs/reference/pairwise_matrix_similarity.html b/docs/reference/pairwise_matrix_similarity.html index b291f8cc..f864a6d4 100644 --- a/docs/reference/pairwise_matrix_similarity.html +++ b/docs/reference/pairwise_matrix_similarity.html @@ -32,7 +32,7 @@
                                                                                                                                                                diff --git a/docs/reference/partialVolumeCorrection.html b/docs/reference/partialVolumeCorrection.html index 2b83a912..65188c9e 100644 --- a/docs/reference/partialVolumeCorrection.html +++ b/docs/reference/partialVolumeCorrection.html @@ -35,7 +35,7 @@
                                                                                                                                                                  diff --git a/docs/reference/perfusionregression.html b/docs/reference/perfusionregression.html index 3cef04a2..2fb8a514 100644 --- a/docs/reference/perfusionregression.html +++ b/docs/reference/perfusionregression.html @@ -32,7 +32,7 @@
                                                                                                                                                                    diff --git a/docs/reference/petSUVR.html b/docs/reference/petSUVR.html index 6606f37a..ae0f2d09 100644 --- a/docs/reference/petSUVR.html +++ b/docs/reference/petSUVR.html @@ -38,7 +38,7 @@
                                                                                                                                                                      diff --git a/docs/reference/plot.antsImage.html b/docs/reference/plot.antsImage.html index 0283743a..0d6bdcf8 100644 --- a/docs/reference/plot.antsImage.html +++ b/docs/reference/plot.antsImage.html @@ -34,7 +34,7 @@
                                                                                                                                                                        diff --git a/docs/reference/plotBasicNetwork.html b/docs/reference/plotBasicNetwork.html index a3665e15..b7dc8792 100644 --- a/docs/reference/plotBasicNetwork.html +++ b/docs/reference/plotBasicNetwork.html @@ -33,7 +33,7 @@
                                                                                                                                                                          diff --git a/docs/reference/plotPrettyGraph.html b/docs/reference/plotPrettyGraph.html index fc99eeb5..4df58336 100644 --- a/docs/reference/plotPrettyGraph.html +++ b/docs/reference/plotPrettyGraph.html @@ -33,7 +33,7 @@
                                                                                                                                                                            @@ -129,7 +129,7 @@

                                                                                                                                                                            Examples

                                                                                                                                                                            #> copyright (c) 2005, Carter T. Butts, University of California-Irvine #> For citation information, type citation("sna"). #> Type help(package="sna") to get started. -#> [1] "/tmp//RtmpBITJNu/file7fff15945084.png" +#> [1] "/tmp//Rtmp2miWxn/file8ddc30154f69.png" diff --git a/docs/reference/powers_areal_mni_itk.html b/docs/reference/powers_areal_mni_itk.html index c467d025..1002bdb6 100644 --- a/docs/reference/powers_areal_mni_itk.html +++ b/docs/reference/powers_areal_mni_itk.html @@ -34,7 +34,7 @@
                                                                                                                                                                              diff --git a/docs/reference/predictSimlr.html b/docs/reference/predictSimlr.html index a7c98fc0..a1ce18c6 100644 --- a/docs/reference/predictSimlr.html +++ b/docs/reference/predictSimlr.html @@ -32,7 +32,7 @@
                                                                                                                                                                                diff --git a/docs/reference/preprocessRestingBOLD.html b/docs/reference/preprocessRestingBOLD.html index b48a5a47..7c11a04f 100644 --- a/docs/reference/preprocessRestingBOLD.html +++ b/docs/reference/preprocessRestingBOLD.html @@ -33,7 +33,7 @@
                                                                                                                                                                                  diff --git a/docs/reference/preprocessfMRI.html b/docs/reference/preprocessfMRI.html index 01dc647e..a63164f1 100644 --- a/docs/reference/preprocessfMRI.html +++ b/docs/reference/preprocessfMRI.html @@ -33,7 +33,7 @@
                                                                                                                                                                                    diff --git a/docs/reference/priorBasedSegmentation.html b/docs/reference/priorBasedSegmentation.html index d5be361a..afa039ea 100644 --- a/docs/reference/priorBasedSegmentation.html +++ b/docs/reference/priorBasedSegmentation.html @@ -33,7 +33,7 @@
                                                                                                                                                                                      diff --git a/docs/reference/quantifyCBF.html b/docs/reference/quantifyCBF.html index 980fbc3c..4d79ff3e 100644 --- a/docs/reference/quantifyCBF.html +++ b/docs/reference/quantifyCBF.html @@ -32,7 +32,7 @@
                                                                                                                                                                                        diff --git a/docs/reference/quantifySNPs.html b/docs/reference/quantifySNPs.html index cc7b8f79..e92ff293 100644 --- a/docs/reference/quantifySNPs.html +++ b/docs/reference/quantifySNPs.html @@ -32,7 +32,7 @@
                                                                                                                                                                                          diff --git a/docs/reference/quantile.antsImage.html b/docs/reference/quantile.antsImage.html index 4462e39e..4ae0110b 100644 --- a/docs/reference/quantile.antsImage.html +++ b/docs/reference/quantile.antsImage.html @@ -33,7 +33,7 @@
                                                                                                                                                                                            @@ -90,7 +90,7 @@

                                                                                                                                                                                            Examples

                                                                                                                                                                                            mask <- img > 0 quantile(img, mask = mask) #> 0% 25% 50% 75% 100% -#> 0.02704368 0.27065562 0.63341951 0.91105765 2.61811447 +#> 0.02098359 0.20460480 0.72204217 1.30325225 2.29307890 diff --git a/docs/reference/randcca.html b/docs/reference/randcca.html index c25764d4..1a6e9f92 100644 --- a/docs/reference/randcca.html +++ b/docs/reference/randcca.html @@ -32,7 +32,7 @@
                                                                                                                                                                                              diff --git a/docs/reference/randomMask.html b/docs/reference/randomMask.html index 2df398e1..8990783e 100644 --- a/docs/reference/randomMask.html +++ b/docs/reference/randomMask.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                diff --git a/docs/reference/randsvd.html b/docs/reference/randsvd.html index 50ce17e7..d28d61b0 100644 --- a/docs/reference/randsvd.html +++ b/docs/reference/randsvd.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                  diff --git a/docs/reference/randwhiten.html b/docs/reference/randwhiten.html index 299d2fac..4ec3ae51 100644 --- a/docs/reference/randwhiten.html +++ b/docs/reference/randwhiten.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                    diff --git a/docs/reference/rankBasedMatrixSegmentation.html b/docs/reference/rankBasedMatrixSegmentation.html index bd0f7b20..0eac4ad0 100644 --- a/docs/reference/rankBasedMatrixSegmentation.html +++ b/docs/reference/rankBasedMatrixSegmentation.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                      diff --git a/docs/reference/rankIntensity.html b/docs/reference/rankIntensity.html index 3b577701..516a9b26 100644 --- a/docs/reference/rankIntensity.html +++ b/docs/reference/rankIntensity.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                        diff --git a/docs/reference/rapidlyInspectImageData.html b/docs/reference/rapidlyInspectImageData.html index 5313855d..4af9dc49 100644 --- a/docs/reference/rapidlyInspectImageData.html +++ b/docs/reference/rapidlyInspectImageData.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                          diff --git a/docs/reference/readAntsrTransform.html b/docs/reference/readAntsrTransform.html index 0c1c14bc..e4ef77b5 100644 --- a/docs/reference/readAntsrTransform.html +++ b/docs/reference/readAntsrTransform.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                            diff --git a/docs/reference/readNormalizedPopulationData.html b/docs/reference/readNormalizedPopulationData.html index ce7970dd..a68e6e3a 100644 --- a/docs/reference/readNormalizedPopulationData.html +++ b/docs/reference/readNormalizedPopulationData.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                              diff --git a/docs/reference/reflectImage.html b/docs/reference/reflectImage.html index b629d460..928e071c 100644 --- a/docs/reference/reflectImage.html +++ b/docs/reference/reflectImage.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                diff --git a/docs/reference/reflectionMatrix.html b/docs/reference/reflectionMatrix.html index 839a0e14..a278d459 100644 --- a/docs/reference/reflectionMatrix.html +++ b/docs/reference/reflectionMatrix.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                  diff --git a/docs/reference/regressProjections.html b/docs/reference/regressProjections.html index ebf128c7..a52e39bc 100644 --- a/docs/reference/regressProjections.html +++ b/docs/reference/regressProjections.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                    diff --git a/docs/reference/regularizeSimlr.html b/docs/reference/regularizeSimlr.html index 553948d8..9024935f 100644 --- a/docs/reference/regularizeSimlr.html +++ b/docs/reference/regularizeSimlr.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                      diff --git a/docs/reference/reho.html b/docs/reference/reho.html index c4a75cbb..8549ff5c 100644 --- a/docs/reference/reho.html +++ b/docs/reference/reho.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                        diff --git a/docs/reference/renormalizeProbabilityImages.html b/docs/reference/renormalizeProbabilityImages.html index 776c84a6..70c94c98 100644 --- a/docs/reference/renormalizeProbabilityImages.html +++ b/docs/reference/renormalizeProbabilityImages.html @@ -37,7 +37,7 @@
                                                                                                                                                                                                                          diff --git a/docs/reference/reorientImage.html b/docs/reference/reorientImage.html index be5b46a1..2ad531d2 100644 --- a/docs/reference/reorientImage.html +++ b/docs/reference/reorientImage.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                            diff --git a/docs/reference/resampleImage.html b/docs/reference/resampleImage.html index 9b982c70..b6423497 100644 --- a/docs/reference/resampleImage.html +++ b/docs/reference/resampleImage.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                              diff --git a/docs/reference/resampleImageToTarget.html b/docs/reference/resampleImageToTarget.html index 9c818c7b..706b8a9b 100644 --- a/docs/reference/resampleImageToTarget.html +++ b/docs/reference/resampleImageToTarget.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                diff --git a/docs/reference/resels.html b/docs/reference/resels.html index 7623b636..b4b06adf 100644 --- a/docs/reference/resels.html +++ b/docs/reference/resels.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                  diff --git a/docs/reference/rfSegmentation.html b/docs/reference/rfSegmentation.html index 83094001..b9c2fa2e 100644 --- a/docs/reference/rfSegmentation.html +++ b/docs/reference/rfSegmentation.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                    diff --git a/docs/reference/rfSegmentationPredict.html b/docs/reference/rfSegmentationPredict.html index cc42dfa2..11211fcd 100644 --- a/docs/reference/rfSegmentationPredict.html +++ b/docs/reference/rfSegmentationPredict.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                      diff --git a/docs/reference/rftPval.html b/docs/reference/rftPval.html index edee3e1e..412888c1 100644 --- a/docs/reference/rftPval.html +++ b/docs/reference/rftPval.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                        diff --git a/docs/reference/rftResults.html b/docs/reference/rftResults.html index 380f5fc6..02e0156b 100644 --- a/docs/reference/rftResults.html +++ b/docs/reference/rftResults.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                          diff --git a/docs/reference/ri.html b/docs/reference/ri.html index b9c47c72..a0609eb3 100644 --- a/docs/reference/ri.html +++ b/docs/reference/ri.html @@ -35,7 +35,7 @@
                                                                                                                                                                                                                                            diff --git a/docs/reference/robustMatrixTransform.html b/docs/reference/robustMatrixTransform.html index 9c818bbb..abdedb72 100644 --- a/docs/reference/robustMatrixTransform.html +++ b/docs/reference/robustMatrixTransform.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                              diff --git a/docs/reference/rsfDenoise.html b/docs/reference/rsfDenoise.html index 4f6219de..f33fd69c 100644 --- a/docs/reference/rsfDenoise.html +++ b/docs/reference/rsfDenoise.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                diff --git a/docs/reference/rvcoef.html b/docs/reference/rvcoef.html index c13720ba..a6e78d01 100644 --- a/docs/reference/rvcoef.html +++ b/docs/reference/rvcoef.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                  diff --git a/docs/reference/save.ANTsR.html b/docs/reference/save.ANTsR.html index b50cbfd1..cc011fad 100644 --- a/docs/reference/save.ANTsR.html +++ b/docs/reference/save.ANTsR.html @@ -40,7 +40,7 @@
                                                                                                                                                                                                                                                    diff --git a/docs/reference/sd.html b/docs/reference/sd.html index dc9924cf..3143014f 100644 --- a/docs/reference/sd.html +++ b/docs/reference/sd.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                      diff --git a/docs/reference/segmentShapeFromImage.html b/docs/reference/segmentShapeFromImage.html index ef63435b..5d034d4c 100644 --- a/docs/reference/segmentShapeFromImage.html +++ b/docs/reference/segmentShapeFromImage.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                        diff --git a/docs/reference/segmentationRefinement.predict.html b/docs/reference/segmentationRefinement.predict.html index 7c54a5ab..c4debbb4 100644 --- a/docs/reference/segmentationRefinement.predict.html +++ b/docs/reference/segmentationRefinement.predict.html @@ -38,7 +38,7 @@
                                                                                                                                                                                                                                                          diff --git a/docs/reference/segmentationRefinement.train.html b/docs/reference/segmentationRefinement.train.html index ee4058ba..57db2cd5 100644 --- a/docs/reference/segmentationRefinement.train.html +++ b/docs/reference/segmentationRefinement.train.html @@ -36,7 +36,7 @@
                                                                                                                                                                                                                                                            diff --git a/docs/reference/setAntsrTransformFixedParameters.html b/docs/reference/setAntsrTransformFixedParameters.html index 188798c0..85ff4581 100644 --- a/docs/reference/setAntsrTransformFixedParameters.html +++ b/docs/reference/setAntsrTransformFixedParameters.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                              diff --git a/docs/reference/setAntsrTransformParameters.html b/docs/reference/setAntsrTransformParameters.html index 880a8477..529a8525 100644 --- a/docs/reference/setAntsrTransformParameters.html +++ b/docs/reference/setAntsrTransformParameters.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                diff --git a/docs/reference/simlr.html b/docs/reference/simlr.html index c10c76f2..35f74e3e 100644 --- a/docs/reference/simlr.html +++ b/docs/reference/simlr.html @@ -40,7 +40,7 @@
                                                                                                                                                                                                                                                                  @@ -83,7 +83,7 @@

                                                                                                                                                                                                                                                                  Similarity-driven multiview linear reconstruction model (simlr) for N modali lineSearchRange = c(-1e+10, 1e+10), lineSearchTolerance = 1e-08, randomSeed, - constraint = c("none", "Grassmann", "Stiefel"), + constraint = c("Grassmannx1000x1000", "Stiefelx1000x1000", "orthox1000x1000", "none"), energyType = c("cca", "regression", "normalized", "ucca", "lowRank", "lowRankRegression"), vmats, diff --git a/docs/reference/simlr.parameters.html b/docs/reference/simlr.parameters.html index 54c648cc..9889c43c 100644 --- a/docs/reference/simlr.parameters.html +++ b/docs/reference/simlr.parameters.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                    diff --git a/docs/reference/simlr.perm.html b/docs/reference/simlr.perm.html index 449a12b5..959294a0 100644 --- a/docs/reference/simlr.perm.html +++ b/docs/reference/simlr.perm.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                      diff --git a/docs/reference/simlr.search.html b/docs/reference/simlr.search.html index 6c895225..1087eafb 100644 --- a/docs/reference/simlr.search.html +++ b/docs/reference/simlr.search.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                        diff --git a/docs/reference/simlrU.html b/docs/reference/simlrU.html index 5128666a..096def8c 100644 --- a/docs/reference/simlrU.html +++ b/docs/reference/simlrU.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                                                          diff --git a/docs/reference/simlr_path_models.html b/docs/reference/simlr_path_models.html index aa0f2530..8b0d825d 100644 --- a/docs/reference/simlr_path_models.html +++ b/docs/reference/simlr_path_models.html @@ -35,7 +35,7 @@
                                                                                                                                                                                                                                                                            diff --git a/docs/reference/simulateDisplacementField.html b/docs/reference/simulateDisplacementField.html index b497d630..24ca5854 100644 --- a/docs/reference/simulateDisplacementField.html +++ b/docs/reference/simulateDisplacementField.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                              diff --git a/docs/reference/skeletonize.html b/docs/reference/skeletonize.html index 7a77e37a..08d573e0 100644 --- a/docs/reference/skeletonize.html +++ b/docs/reference/skeletonize.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                                                                diff --git a/docs/reference/smoothAppGradCCA.html b/docs/reference/smoothAppGradCCA.html index 3196353d..b4351c7a 100644 --- a/docs/reference/smoothAppGradCCA.html +++ b/docs/reference/smoothAppGradCCA.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                  diff --git a/docs/reference/smoothImage.html b/docs/reference/smoothImage.html index 40961c6f..3067c71e 100644 --- a/docs/reference/smoothImage.html +++ b/docs/reference/smoothImage.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                    diff --git a/docs/reference/smoothMatrixPrediction.html b/docs/reference/smoothMatrixPrediction.html index 6e98dca8..e2bdee8f 100644 --- a/docs/reference/smoothMatrixPrediction.html +++ b/docs/reference/smoothMatrixPrediction.html @@ -36,7 +36,7 @@
                                                                                                                                                                                                                                                                                      diff --git a/docs/reference/smoothMultiRegression.html b/docs/reference/smoothMultiRegression.html index 11ce37d6..f1b0af3e 100644 --- a/docs/reference/smoothMultiRegression.html +++ b/docs/reference/smoothMultiRegression.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                        diff --git a/docs/reference/smoothRegression.html b/docs/reference/smoothRegression.html index ec478c84..fc2b0948 100644 --- a/docs/reference/smoothRegression.html +++ b/docs/reference/smoothRegression.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                          diff --git a/docs/reference/sparseDecom.html b/docs/reference/sparseDecom.html index 825c53e8..002a9533 100644 --- a/docs/reference/sparseDecom.html +++ b/docs/reference/sparseDecom.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                                                                            diff --git a/docs/reference/sparseDecom2.html b/docs/reference/sparseDecom2.html index c97f06db..32a44b15 100644 --- a/docs/reference/sparseDecom2.html +++ b/docs/reference/sparseDecom2.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                                                                              diff --git a/docs/reference/sparseDecom2boot.html b/docs/reference/sparseDecom2boot.html index 5bd3c644..a84790bd 100644 --- a/docs/reference/sparseDecom2boot.html +++ b/docs/reference/sparseDecom2boot.html @@ -35,7 +35,7 @@
                                                                                                                                                                                                                                                                                                diff --git a/docs/reference/sparseDecomboot.html b/docs/reference/sparseDecomboot.html index 3bd315ec..a813892a 100644 --- a/docs/reference/sparseDecomboot.html +++ b/docs/reference/sparseDecomboot.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                                  diff --git a/docs/reference/sparseDistanceMatrix.html b/docs/reference/sparseDistanceMatrix.html index b01009df..7d7a5b3f 100644 --- a/docs/reference/sparseDistanceMatrix.html +++ b/docs/reference/sparseDistanceMatrix.html @@ -36,7 +36,7 @@
                                                                                                                                                                                                                                                                                                    diff --git a/docs/reference/sparseDistanceMatrixXY.html b/docs/reference/sparseDistanceMatrixXY.html index 77a4c4c3..56051441 100644 --- a/docs/reference/sparseDistanceMatrixXY.html +++ b/docs/reference/sparseDistanceMatrixXY.html @@ -37,7 +37,7 @@
                                                                                                                                                                                                                                                                                                      diff --git a/docs/reference/sparseRegression.html b/docs/reference/sparseRegression.html index 40081476..e0d28a19 100644 --- a/docs/reference/sparseRegression.html +++ b/docs/reference/sparseRegression.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                                        diff --git a/docs/reference/spatialbayesianlm.html b/docs/reference/spatialbayesianlm.html index b56d11d4..9fbd575d 100644 --- a/docs/reference/spatialbayesianlm.html +++ b/docs/reference/spatialbayesianlm.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                                          diff --git a/docs/reference/splitChannels.html b/docs/reference/splitChannels.html index 7f4be1a7..811a9a89 100644 --- a/docs/reference/splitChannels.html +++ b/docs/reference/splitChannels.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                            diff --git a/docs/reference/splitData.html b/docs/reference/splitData.html index 8711ff02..871d4c2a 100644 --- a/docs/reference/splitData.html +++ b/docs/reference/splitData.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                              diff --git a/docs/reference/splitMask.html b/docs/reference/splitMask.html index cdb2ebe9..9bcad483 100644 --- a/docs/reference/splitMask.html +++ b/docs/reference/splitMask.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                diff --git a/docs/reference/splitNDImageToList.html b/docs/reference/splitNDImageToList.html index 46dd54dd..61813c5e 100644 --- a/docs/reference/splitNDImageToList.html +++ b/docs/reference/splitNDImageToList.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                                                  diff --git a/docs/reference/statFieldThresh.html b/docs/reference/statFieldThresh.html index 66e11b3d..a3703018 100644 --- a/docs/reference/statFieldThresh.html +++ b/docs/reference/statFieldThresh.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                    diff --git a/docs/reference/subgradientL1Regression.html b/docs/reference/subgradientL1Regression.html index e320165a..9db290e8 100644 --- a/docs/reference/subgradientL1Regression.html +++ b/docs/reference/subgradientL1Regression.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                      diff --git a/docs/reference/subjectDataToGroupDataFrame.html b/docs/reference/subjectDataToGroupDataFrame.html index 3da443cb..6c8a6652 100644 --- a/docs/reference/subjectDataToGroupDataFrame.html +++ b/docs/reference/subjectDataToGroupDataFrame.html @@ -34,7 +34,7 @@
                                                                                                                                                                                                                                                                                                                        diff --git a/docs/reference/subset.html b/docs/reference/subset.html index 174086d6..fb77cc55 100644 --- a/docs/reference/subset.html +++ b/docs/reference/subset.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                          diff --git a/docs/reference/take_abs_unsigned.html b/docs/reference/take_abs_unsigned.html index 0a3e33d9..62811cc1 100644 --- a/docs/reference/take_abs_unsigned.html +++ b/docs/reference/take_abs_unsigned.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                            diff --git a/docs/reference/taskFMRI.html b/docs/reference/taskFMRI.html index 0dc044e6..369237ad 100644 --- a/docs/reference/taskFMRI.html +++ b/docs/reference/taskFMRI.html @@ -37,7 +37,7 @@
                                                                                                                                                                                                                                                                                                                              diff --git a/docs/reference/temporalwhiten.html b/docs/reference/temporalwhiten.html index eaee6d17..6f0d0953 100644 --- a/docs/reference/temporalwhiten.html +++ b/docs/reference/temporalwhiten.html @@ -33,7 +33,7 @@
                                                                                                                                                                                                                                                                                                                                diff --git a/docs/reference/testEanat.html b/docs/reference/testEanat.html index 860a8bd9..3d06a932 100644 --- a/docs/reference/testEanat.html +++ b/docs/reference/testEanat.html @@ -38,7 +38,7 @@
                                                                                                                                                                                                                                                                                                                                  diff --git a/docs/reference/thresholdImage.html b/docs/reference/thresholdImage.html index f349b02e..755095cc 100644 --- a/docs/reference/thresholdImage.html +++ b/docs/reference/thresholdImage.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                                    diff --git a/docs/reference/timeseries2matrix.html b/docs/reference/timeseries2matrix.html index 7f26fef2..6b8395d7 100644 --- a/docs/reference/timeseries2matrix.html +++ b/docs/reference/timeseries2matrix.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                                      diff --git a/docs/reference/timeseriesN3.html b/docs/reference/timeseriesN3.html index 1105ef1b..48855e4b 100644 --- a/docs/reference/timeseriesN3.html +++ b/docs/reference/timeseriesN3.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                                        diff --git a/docs/reference/timeserieswindow2matrix.html b/docs/reference/timeserieswindow2matrix.html index 11da0ca3..2042e06f 100644 --- a/docs/reference/timeserieswindow2matrix.html +++ b/docs/reference/timeserieswindow2matrix.html @@ -33,7 +33,7 @@
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                                                                                                                                                                                                                                                                                                                                                      Examples

                                                                                                                                                                                                                                                                                                                                                      #> Pearson's product-moment correlation #> #> data: vv2 and vv -#> t = Inf, df = 1948, p-value < 2.2e-16 +#> t = 2961927088, df = 1948, p-value < 2.2e-16 #> alternative hypothesis: true correlation is not equal to 0 #> 95 percent confidence interval: #> 1 1 diff --git a/docs/reference/vector_to_df.html b/docs/reference/vector_to_df.html index 5bfb09fb..7e30a928 100644 --- a/docs/reference/vector_to_df.html +++ b/docs/reference/vector_to_df.html @@ -32,7 +32,7 @@
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                                                                                                                                                                                                                                                                                                                                                                    diff --git a/docs/reference/writeAntsrTransform.html b/docs/reference/writeAntsrTransform.html index 4ebbd2f1..36db206e 100644 --- a/docs/reference/writeAntsrTransform.html +++ b/docs/reference/writeAntsrTransform.html @@ -32,7 +32,7 @@
                                                                                                                                                                                                                                                                                                                                                                      diff --git a/docs/reference/writeNormalizedPopulationData.html b/docs/reference/writeNormalizedPopulationData.html index b688b80f..d9a8ca13 100644 --- a/docs/reference/writeNormalizedPopulationData.html +++ b/docs/reference/writeNormalizedPopulationData.html @@ -41,7 +41,7 @@
                                                                                                                                                                                                                                                                                                                                                                        diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 2a159f66..6e5b83a8 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -213,6 +213,24 @@ /reference/antsVersions.html + + /reference/antspymm_nuisance_names.html + + + /reference/antspymm_predictors.html + + + /reference/antspymm_qc_names.html + + + /reference/antspymm_simlr.html + + + /reference/antspymm_simlr_update_residuals.html + + + /reference/antspymm_vartype.html + /reference/antsrGetPointerName.html @@ -450,6 +468,9 @@ /reference/exemplarInpainting.html + + /reference/exploratory_visualization.html + /reference/extractSlice.html @@ -540,6 +561,9 @@ /reference/getfMRInuisanceVariables.html + + /reference/glm_impute.html + /reference/gradient_invariant_orthogonality_defect.html @@ -627,6 +651,12 @@ /reference/interleaveMatrixWithItself.html + + /reference/interpret_simlr_vector.html + + + /reference/interpret_simlr_vector2.html + /reference/invariantImageSimilarity.html @@ -819,6 +849,9 @@ /reference/plotPrettyGraph.html + + /reference/plot_features.html + /reference/powers_areal_mni_itk.html @@ -870,6 +903,9 @@ /reference/readNormalizedPopulationData.html + + /reference/read_simlr_data_frames.html + /reference/reexports.html @@ -957,6 +993,9 @@ /reference/setAntsrTransformParameters.html + + /reference/shorten_pymm_names.html + /reference/simlr.html @@ -975,6 +1014,9 @@ /reference/simlrU.html + + /reference/simlr_impute.html + /reference/simlr_path_models.html @@ -1101,6 +1143,9 @@ /reference/visualize_lowrank_relationships.html + + /reference/visualize_permutation_test.html + /reference/vwnrfs.html @@ -1122,4 +1167,7 @@ /reference/writeNormalizedPopulationData.html + + /reference/write_simlr_data_frames.html +