Man pages for Mouse-Imaging-Centre/RMINC
Statistical Tools for Medical Imaging NetCDF (MINC) Files
| add_colour_bar | Add a colour bar for a mesh |
| add_opacity | Add opacity to a mesh |
| addVolumesToHierarchy | Add volumes to an anatomical hierarchy |
| AICc | Compute the Corrected AIC for an object |
| anatAnova | Performs ANOVA on each region specified |
| anatApply | Apply function over anat structure |
| anatCombineStructures | Combine left and right volumes |
| anatCreateVolume | Create a Statistic Volume |
| anatFDR | Anatomy False Discovery Rates |
| anatGetAll | Faster AnatGet |
| anatGetAll_old | Get values given a set of files and an atlas |
| anatLm | Calculates statistics and coefficients for linear model of... |
| anatLmer | Anatomy Linear Mixed Effects Model |
| anatLmerEstimateDF | Estimate Degrees of freedom for an anatLmer model |
| anatSummaries | anatSummaries |
| anatSummarize | Summarize anatGetAll results by hierarchy |
| anatToVolume | Converts a column from an anatLm model into a volume for... |
| as.data.frame.anatMatrix | Create Anatomy data.frame |
| as.minc | Coerce to RMINC object |
| check_step_sizes | Check file step sizes |
| civet.checkVersion | Check for a known Civet Version |
| civet.computeNativeToStxRescalingFactor | Compute Native to Stereotactic Rescaling Factor |
| civet.computeTissueVolumes | Compute GM, WM, and CSF Tissue Volumes |
| civet.CreateBrainViewFile | Create a brain view file |
| civet.CreateBrainViewROI | civet.CreateBrainViewROI |
| civet.flattenForDplyr | Flatten CIVET results for dplyr |
| civet.getAllFilenames | civet.getAllFilenames |
| civet.getFilename | Get Selected Civet Filenames |
| civet.organizeCivetDatFilesAtlas | Organizes CIVET .dat files based on an Atlas |
| civet.readAllCivetFiles | Read all CIVET files into R |
| civet.readCBRAIN | Read a CBRAIN project in R |
| civet.readCivetDatFiles | Read Civet-Generated Dat Files |
| civet.readQC | Read CIVET QC data |
| civet.vertexFilenames | Assemble vertex files for a CIVET run |
| civet.vertexTable | Create a table of vertex measures |
| clean_up_manifold_triangles | Clean up manifold mesh |
| closestVertex | Find Closest Vertex |
| colour_mesh | Colourize a mesh |
| compare_models | Compare a set of massively-univariate models |
| components_to_map | Components to map |
| connected_components | Find connected components of a object graph |
| create_mesh | Create surface mesh for a bic_obj |
| extract_column | Internal function to read in a table or csv file potentially... |
| getRMINCTestData | Download Example Data |
| hanatAnova | ANOVA applied to every item in an anatomical tree |
| hanatFDR | Compute the False Discovery Rate for an anatomical hierarchy |
| hanatLm | linear model applied to every item in an anatomical tree |
| hanatLmer | linear mixed effects model applied to every item in an... |
| hanatLmerEstimateDF | Estimates degrees of freedom |
| hanatPlot | hanatPlot |
| hanatToVisGraph | Turns an anatomical tree into a nodes and edges for... |
| hanatToVolume | Converts a column from a hierarchical tree into a volume for... |
| is.minc | Check for RMINC objects |
| laplace_beltrami_operator | Compute Laplace-Beltrami operator |
| laplace_beltrami_smoothing | Smoothing on manifold |
| launch_shinyRMINC | launch a shiny based inspector |
| likeVolume | Get or set a likeVolume |
| line_obj_to_voxel | Convert Lines to Voxel Coordinates |
| lut_to_palette | A tool that returns a color function/palette from color... |
| makeMICeDefsHierachical | Creates a hierarchical anatomical tree |
| map_to_colours | Generate a vector of colours from a map |
| maskFile | Get or set a mask file |
| mcMincApply | Local multicore mincApply |
| mincAnova | Voxel-wise ANOVA Compute a sequential ANOVA at each voxel |
| mincApply | Apply arbitrary R function at every voxel |
| mincApplyRCPP | Perform Arbitrary calculations on a collection of mincVolumes |
| mincArray | A utility function to give a MINC object spatial dimensions |
| mincAttributes | Get and Set Minc Specific Attributes |
| mincContour | Draw contour lines from a MINC volume |
| mincConvertTagToMincArrayCoordinates | convert tags from world coordinates to mincArray coordinates |
| mincConvertVoxelMatrix | Convert Voxel to World Coordinates |
| mincConvertVoxelToWorld | Voxel to World |
| mincConvertWorldMatrix | Convert World to Voxel Coordinates |
| mincConvertWorldToVoxel | World to Voxel |
| minc.dimensions.sizes | Dimension Sizes |
| mincFDR | False Discovery Rates |
| mincFDRMask | mincFDRMask |
| mincFDRThresholdVector | a utility function to compute thresholds |
| mincFileCheck | Minc File Check |
| mincFindPeaks | Finds peak values in a MINC file or volume |
| minc.get.hyperslab | Get a hyperslab from a MINC2 file |
| mincGetMask | Minc Masks |
| mincGetTagFile | read a tag file |
| mincGetVector | Voxel Vector |
| mincGetVolume | Read a MINC file |
| mincGetVoxel | Retrieve Voxel Values |
| mincGetWorldVoxel | World Vector |
| minc_history | Minc History |
| mincImage | Plot a slice from a MINC volume |
| mincLabelPeaks | label peaks with the name of the atlas structure they are in |
| mincLm | Linear model at Every Voxel |
| mincLmer | mincified version of lmer from lme4 |
| mincLmerEstimateDF | Estimate the degrees of freedom for parameters in a mincLmer... |
| mincLogLikRatio | run log likelihood ratio tests for different mincLmer objects |
| mincLogLikRatioParametricBootstrap | computes parametric bootstrap on mincLogLikRatio output |
| mincPairedTtest | Minc Paired T Test |
| mincPlotAnatAndStatsSlice | Anatomy and Statistics Slice |
| mincPlotPeak | Plotting of peaks |
| mincPlotSliceSeries | MINC Slice Series |
| mincRandomize | Run a permutation test on a 'mincLm' result |
| minc.ray.trace | Call ray_trace to get an image of a rendered slice |
| mincRayTraceStats | Create an image of a statistical peak. |
| mincSelectRandomVoxels | selects a few random indices from a volume |
| minc.separation.sizes | Slice Separations |
| mincSummary | Minc Voxel Summary Functions |
| mincTable | Read a collection of minc volumes |
| mincTFCE | Threshold Free Cluster Enhancement |
| mincTriplanarSlicePlot | Plot Slice Along Each Axis |
| mincTtest | Minc T-test |
| mincVectorToVoxelCoordinates | converts a vector index to the voxel indices in MINC |
| mincWilcoxon | Minc Wilcoxon |
| mincWriteVolume | Write a MINC volume to file |
| obj_montage | Brain Montage |
| obj_to_graph | Object to Graph |
| plot.bic_lines | Plot A bic_lines object |
| plot.bic_obj | Plot a BIC obj |
| plot.obj_mesh | Plot an BIC obj mesh |
| pMincApply | Parallel MincApply |
| pt2 | Two tailed version of pt |
| qMincApply | True cluster mincApply |
| read_line_obj | Read a BIC-obj line file |
| read_obj | Read BIC .obj files |
| RMINC | RMINC: R interface to the MINC universe |
| RMINC_MASKED_VALUE | RMINC Masked Value |
| runRMINCTestbed | Run Testbed |
| setRMINCMaskedValue | Set Masked Value |
| simplify2minc | Collate Minc |
| simplify_masked | Simplify Masked Results |
| thresholds | Get Probability Thresholds |
| verboseRun | Run function with/without output silenced |
| vertexAnova | Performs ANOVA on each vertex point specified |
| vertexApply | Apply function over vertex Files |
| vertexAtlasApply | Apply a structure summary function across vertices |
| vertexEffectSize | Effect Sizes |
| vertexFDR | Vertex False Discovery Rates |
| vertexFindPeaks | Vertex find peaks |
| vertexLm | Calculates statistics and coefficients for linear model of... |
| vertexLmer | Vertex Mixed Effects Models |
| vertexLmerEstimateDF | Estimate the degrees of freedom for parameters in a... |
| vertexLookup | Vertex Lookup |
| vertexSelect | Select Vertices From a Surface |
| vertexSummaries | Create descriptive statistics across a series of vertex files |
| vertexTable | Create a table of vertex values |
| vertexTFCE | Threshold Free Cluster Enhancement |
| volume.combineMaskVolumes | Combine Multiple Mask Volumes into a Single Mask Volume |
| volume.explodeLabelVolume | Explode a Label Volume into its Components |
| voxel_atlas_defs | Voxel Atlas Definitions |
| writeVertex | Writes vertex data to a file with an optional header |
