Files in Mouse-Imaging-Centre/RMINC
Statistical Tools for Medical Imaging NetCDF (MINC) Files

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
ChangeLog
DESCRIPTION
Gemfile
INSTALL
LICENSE
Makefile
NAMESPACE
NEWS
R/RMINC.R R/RcppExports.R R/civet.R R/minc_FDR.R R/minc_anatomy.R R/minc_graphs.R R/minc_hierarchical_anatomy.R R/minc_interface.R R/minc_lmer.R R/minc_misc.R R/minc_model_selection.R R/minc_parallel.R R/minc_peaks.R R/minc_shiny.R R/minc_vertex_statistics.R R/minc_vis2D.R R/minc_vis3D.R R/minc_voxel_statistics.R
R/sysdata.rda
README
RMINC.Rproj
_config.yml
_pkgdown.yml
cleanup
configure
configure.ac
docs/LICENSE-text.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AICc.html
docs/reference/RMINC.html
docs/reference/RMINC_MASKED_VALUE.html
docs/reference/addVolumesToHierarchy.html
docs/reference/add_colour_bar.html
docs/reference/add_opacity.html
docs/reference/anatAnova.html
docs/reference/anatApply.html
docs/reference/anatCombineStructures.html
docs/reference/anatCreateVolume.html
docs/reference/anatFDR.html
docs/reference/anatGetAll.html
docs/reference/anatGetAll_old.html
docs/reference/anatLm.html
docs/reference/anatLmer.html
docs/reference/anatLmerEstimateDF.html
docs/reference/anatSummaries.html
docs/reference/anatSummarize.html
docs/reference/as.data.frame.anatMatrix.html
docs/reference/as.minc.html
docs/reference/check_step_sizes.html
docs/reference/civet.CreateBrainViewFile.html
docs/reference/civet.CreateBrainViewROI.html
docs/reference/civet.checkVersion.html
docs/reference/civet.computeNativeToStxRescalingFactor.html
docs/reference/civet.computeTissueVolumes.html
docs/reference/civet.flattenForDplyr.html
docs/reference/civet.getAllFilenames.html
docs/reference/civet.getFilename.html
docs/reference/civet.organizeCivetDatFilesAtlas.html
docs/reference/civet.readAllCivetFiles.html
docs/reference/civet.readCBRAIN.html
docs/reference/civet.readCivetDatFiles.html
docs/reference/civet.readQC.html
docs/reference/civet.vertexFilenames.html
docs/reference/civet.vertexTable.html
docs/reference/closestVertex.html
docs/reference/colour_mesh.html
docs/reference/compare_models.html
docs/reference/components_to_map.html
docs/reference/connected_components.html
docs/reference/create_mesh.html
docs/reference/getRMINCTestData.html
docs/reference/hanatAnova.html
docs/reference/hanatFDR.html
docs/reference/hanatLm.html
docs/reference/hanatLmer.html
docs/reference/hanatLmerEstimateDF.html
docs/reference/hanatPlot.html
docs/reference/hanatToVisGraph.html
docs/reference/hanatToVolume.html
docs/reference/index.html
docs/reference/is.minc.html
docs/reference/launch_shinyRMINC.html
docs/reference/likeVolume.html
docs/reference/line_obj_to_voxel.html
docs/reference/lut_to_palette.html
docs/reference/makeMICeDefsHierachical.html
docs/reference/map_to_colours.html
docs/reference/maskFile.html
docs/reference/mcMincApply.html
docs/reference/minc.dimensions.sizes.html
docs/reference/minc.get.hyperslab.html
docs/reference/minc.ray.trace.html
docs/reference/minc.separation.sizes.html
docs/reference/mincAnova.html
docs/reference/mincApply.html
docs/reference/mincApplyRCPP.html
docs/reference/mincArray.html
docs/reference/mincAttributes.html
docs/reference/mincContour.html
docs/reference/mincConvertTagToMincArrayCoordinates.html
docs/reference/mincConvertVoxelMatrix.html
docs/reference/mincConvertVoxelToWorld.html
docs/reference/mincConvertWorldMatrix.html
docs/reference/mincConvertWorldToVoxel.html
docs/reference/mincFDR.html
docs/reference/mincFDRMask.html
docs/reference/mincFDRThresholdVector.html
docs/reference/mincFileCheck.html
docs/reference/mincFindPeaks.html
docs/reference/mincGetMask.html
docs/reference/mincGetTagFile.html
docs/reference/mincGetVector.html
docs/reference/mincGetVolume.html
docs/reference/mincGetVoxel.html
docs/reference/mincGetWorldVoxel.html
docs/reference/mincImage.html
docs/reference/mincLabelPeaks.html
docs/reference/mincLm.html
docs/reference/mincLmer.html
docs/reference/mincLmerEstimateDF.html
docs/reference/mincLogLikRatio.html
docs/reference/mincLogLikRatioParametricBootstrap.html
docs/reference/mincPairedTtest.html
docs/reference/mincPlotAnatAndStatsSlice.html
docs/reference/mincPlotPeak.html
docs/reference/mincPlotSliceSeries.html
docs/reference/mincRandomize.html
docs/reference/mincRayTraceStats.html
docs/reference/mincSelectRandomVoxels.html
docs/reference/mincSummary.html
docs/reference/mincTFCE.html
docs/reference/mincTriplanarSlicePlot.html
docs/reference/mincTtest.html
docs/reference/mincVectorToVoxelCoordinates.html
docs/reference/mincWilcoxon.html
docs/reference/mincWriteVolume.html
docs/reference/minc_history.html
docs/reference/obj_montage.html
docs/reference/obj_to_graph.html
docs/reference/pMincApply.html
docs/reference/plot.bic_lines.html
docs/reference/plot.bic_obj.html
docs/reference/plot.obj_mesh.html
docs/reference/pt2.html
docs/reference/qMincApply.html
docs/reference/read_line_obj.html
docs/reference/read_obj.html
docs/reference/runRMINCTestbed.html
docs/reference/setRMINCMaskedValue.html
docs/reference/simplify2minc.html
docs/reference/simplify_masked.html
docs/reference/thresholds.html
docs/reference/verboseRun.html
docs/reference/vertexAnova.html
docs/reference/vertexApply.html
docs/reference/vertexFDR.html
docs/reference/vertexFindPeaks.html
docs/reference/vertexLm.html
docs/reference/vertexLmer.html
docs/reference/vertexLmerEstimateDF.html
docs/reference/vertexLookup.html
docs/reference/vertexSelect.html
docs/reference/vertexSummaries.html
docs/reference/vertexTFCE.html
docs/reference/vertexTable.html
docs/reference/volume.combineMaskVolumes.html
docs/reference/volume.explodeLabelVolume.html
docs/reference/voxel_atlas_defs.html
docs/reference/writeVertex.html
etc/file_io_experiments.R etc/hanat-testing.Rmd
etc/hanat-testing.nb.html
etc/mincLm_benchmarking.Rmd
etc/mincLm_benchmarking.html
etc/mincTFCE_experiments.R etc/more_vtfce_tests.R etc/test_torque_parallel.R etc/vertexTFCE_experiments.R etc/vertexTests.R index.Rmd
inst/CITATION
inst/civet_extras/CIVET_2.0_AAL_labels.txt
inst/civet_extras/CIVET_2.0_DKT_labels.txt
inst/civet_extras/CIVET_2.1_AAL_labels.txt
inst/civet_extras/CIVET_2.1_AAL_left.txt
inst/civet_extras/CIVET_2.1_AAL_right.txt
inst/documentation/RMINC-userGuide.Rnw
inst/documentation/RMINC-userGuide.pdf inst/documentation/RMINC_Parallelism.Rmd
inst/documentation/RMINC_Parallelism.html
inst/documentation/RMINC_rgl.Rmd
inst/documentation/RMINC_rgl.html
inst/documentation/RMINC_rgl_data/selected_vertices.png
inst/documentation/VBMstats.Rnw
inst/documentation/VBMstats.pdf inst/documentation/hierarchiesTutorial.Rmd
inst/documentation/hierarchiesTutorial.html
inst/documentation/visualizationTutorial.Rmd
inst/documentation/visualizationTutorial.html
inst/luts/blue
inst/luts/bluered
inst/luts/bluered_4sd
inst/luts/cyan
inst/luts/gray
inst/luts/green
inst/luts/half_hotblue
inst/luts/half_hotgreen
inst/luts/half_hotred
inst/luts/hotblue
inst/luts/hotgreen
inst/luts/hotmetal
inst/luts/hotred
inst/luts/hotrednowhite
inst/luts/labels.map
inst/luts/magenta
inst/luts/phase
inst/luts/pt_blue
inst/luts/pt_green
inst/luts/pt_red
inst/luts/red
inst/luts/spectral
inst/luts/yellow
inst/parallel/MICe_BatchJobs.R inst/parallel/pbs_batchtools.R
inst/parallel/pbs_script.tmpl
inst/parallel/sge_batchtools.R
inst/parallel/sge_script.tmpl
inst/parallel/slurm_batchtools.R
inst/parallel/slurm_script.tmpl
inst/shinyRMINC/server.R inst/shinyRMINC/ui.R
inst/tools/ax_lib_hdf5.m4
inst/tools/ch_minc_depends.m4
inst/user_tests/test_anatAnova.R inst/user_tests/test_anatApply.R inst/user_tests/test_anatFDR.R inst/user_tests/test_anatGet.R inst/user_tests/test_anatLm.R inst/user_tests/test_anatLmer.R inst/user_tests/test_anatomy.R inst/user_tests/test_civet.R inst/user_tests/test_mincAnova.R inst/user_tests/test_mincApply.R inst/user_tests/test_mincFDR.R inst/user_tests/test_mincLm.R inst/user_tests/test_mincLmer.R inst/user_tests/test_mincSummary.R inst/user_tests/test_mincTFCE.R inst/user_tests/test_minc_apply_rcpp.R inst/user_tests/test_misc.R inst/user_tests/test_objects.R inst/user_tests/test_qminc.R inst/user_tests/test_vertexAnova.R inst/user_tests/test_vertexApply.R inst/user_tests/test_vertexFDR.R inst/user_tests/test_vertexLm.R inst/user_tests/test_vertexSummary.R inst/user_tests/test_vertex_lmer.R inst/user_tests/test_visualizations.R man/AICc.Rd man/RMINC.Rd man/RMINC_MASKED_VALUE.Rd man/addVolumesToHierarchy.Rd man/add_colour_bar.Rd man/add_opacity.Rd man/anatAnova.Rd man/anatApply.Rd man/anatCombineStructures.Rd man/anatCreateVolume.Rd man/anatFDR.Rd man/anatGetAll.Rd man/anatGetAll_old.Rd man/anatLm.Rd man/anatLmer.Rd man/anatLmerEstimateDF.Rd man/anatSummaries.Rd man/anatSummarize.Rd man/as.data.frame.anatMatrix.Rd man/as.minc.Rd man/check_step_sizes.Rd man/civet.CreateBrainViewFile.Rd man/civet.CreateBrainViewROI.Rd man/civet.checkVersion.Rd man/civet.computeNativeToStxRescalingFactor.Rd man/civet.computeTissueVolumes.Rd man/civet.flattenForDplyr.Rd man/civet.getAllFilenames.Rd man/civet.getFilename.Rd man/civet.organizeCivetDatFilesAtlas.Rd man/civet.readAllCivetFiles.Rd man/civet.readCBRAIN.Rd man/civet.readCivetDatFiles.Rd man/civet.readQC.Rd man/civet.vertexFilenames.Rd man/civet.vertexTable.Rd man/closestVertex.Rd man/colour_mesh.Rd man/compare_models.Rd man/components_to_map.Rd man/connected_components.Rd man/create_mesh.Rd man/getRMINCTestData.Rd man/hanatAnova.Rd man/hanatFDR.Rd man/hanatLm.Rd man/hanatLmer.Rd man/hanatLmerEstimateDF.Rd man/hanatPlot.Rd man/hanatToVisGraph.Rd man/hanatToVolume.Rd man/is.minc.Rd man/launch_shinyRMINC.Rd man/likeVolume.Rd man/line_obj_to_voxel.Rd man/lut_to_palette.Rd man/makeMICeDefsHierachical.Rd man/map_to_colours.Rd man/maskFile.Rd man/mcMincApply.Rd man/minc.dimensions.sizes.Rd man/minc.get.hyperslab.Rd man/minc.ray.trace.Rd man/minc.separation.sizes.Rd man/mincAnova.Rd man/mincApply.Rd man/mincApplyRCPP.Rd man/mincArray.Rd man/mincAttributes.Rd man/mincContour.Rd man/mincConvertTagToMincArrayCoordinates.Rd man/mincConvertVoxelMatrix.Rd man/mincConvertVoxelToWorld.Rd man/mincConvertWorldMatrix.Rd man/mincConvertWorldToVoxel.Rd man/mincFDR.Rd man/mincFDRMask.Rd man/mincFDRThresholdVector.Rd man/mincFileCheck.Rd man/mincFindPeaks.Rd man/mincGetMask.Rd man/mincGetTagFile.Rd man/mincGetVector.Rd man/mincGetVolume.Rd man/mincGetVoxel.Rd man/mincGetWorldVoxel.Rd man/mincImage.Rd man/mincLabelPeaks.Rd man/mincLm.Rd man/mincLmer.Rd man/mincLmerEstimateDF.Rd man/mincLogLikRatio.Rd man/mincLogLikRatioParametricBootstrap.Rd man/mincPairedTtest.Rd man/mincPlotAnatAndStatsSlice.Rd man/mincPlotPeak.Rd man/mincPlotSliceSeries.Rd man/mincRandomize.Rd man/mincRayTraceStats.Rd man/mincSelectRandomVoxels.Rd man/mincSummary.Rd man/mincTFCE.Rd man/mincTriplanarSlicePlot.Rd man/mincTtest.Rd man/mincVectorToVoxelCoordinates.Rd man/mincWilcoxon.Rd man/mincWriteVolume.Rd man/minc_history.Rd man/obj_montage.Rd man/obj_to_graph.Rd man/pMincApply.Rd man/plot.bic_lines.Rd man/plot.bic_obj.Rd man/plot.obj_mesh.Rd man/pt2.Rd man/qMincApply.Rd man/read_line_obj.Rd man/read_obj.Rd man/runRMINCTestbed.Rd man/setRMINCMaskedValue.Rd man/simplify2minc.Rd man/simplify_masked.Rd man/thresholds.Rd man/verboseRun.Rd man/vertexAnova.Rd man/vertexApply.Rd man/vertexFDR.Rd man/vertexFindPeaks.Rd man/vertexLm.Rd man/vertexLmer.Rd man/vertexLmerEstimateDF.Rd man/vertexLookup.Rd man/vertexSelect.Rd man/vertexSummaries.Rd man/vertexTFCE.Rd man/vertexTable.Rd man/volume.combineMaskVolumes.Rd man/volume.explodeLabelVolume.Rd man/voxel_atlas_defs.Rd man/writeVertex.Rd
src/Makevars.in
src/RMINC_init.c
src/RcppExports.cpp
src/anat_summaries.cpp
src/minc2_io.h
src/minc2_read.c
src/minc2_support.c
src/minc2_write.c
src/minc_anova.c
src/minc_apply.cpp
src/minc_cpp.cpp
src/minc_cpp.h
src/minc_reader.c
src/minc_reader.h
src/modelling_functions.c
src/modelling_functions.h
src/slice_loop.h
src/slice_loop_functions.c
src/utilities.cpp
src/vertex_modelling.c
src/vertex_tfce.cpp
src/weighted_least_squares.c
tests/testthat.R tests/testthat/test_anatAnova.R tests/testthat/test_anatApply.R tests/testthat/test_anatFDR.R tests/testthat/test_anatGet.R tests/testthat/test_anatLm.R tests/testthat/test_anatLmer.R tests/testthat/test_anatomy.R tests/testthat/test_civet.R tests/testthat/test_mincAnova.R tests/testthat/test_mincApply.R tests/testthat/test_mincFDR.R tests/testthat/test_mincLm.R tests/testthat/test_mincLmer.R tests/testthat/test_mincSummary.R tests/testthat/test_mincTFCE.R tests/testthat/test_minc_apply_rcpp.R tests/testthat/test_misc.R tests/testthat/test_objects.R tests/testthat/test_qminc.R tests/testthat/test_vertexAnova.R tests/testthat/test_vertexApply.R tests/testthat/test_vertexFDR.R tests/testthat/test_vertexLm.R tests/testthat/test_vertexSummary.R tests/testthat/test_vertex_lmer.R tests/testthat/test_visualizations.R
Mouse-Imaging-Centre/RMINC documentation built on Oct. 5, 2018, 9:23 a.m.