_pkgdown.yml

url: https://bbuchsbaum.github.io/neuroim2/
template:
  bootstrap: 5
  package: albersdown
articles:
- title: Start Here
  desc: The shortest path from reading data to understanding space and storage
  contents:
  - Overview
  - ChoosingBackends
  - coordinate-systems
  - VolumesAndVectors
  - Resampling
- title: Analysis Workflows
  desc: Common analysis patterns built from ROIs, searchlights, and summaries
  contents:
  - AnalysisWorkflows
  - slice-visualization
  - Cookbook
- title: Spatial Workflows
  desc: Focused spatial methods outside the main onboarding path
  contents: Smoothing
- title: Advanced Topics
  desc: Deeper or more specialized articles beyond the main reader path
  contents:
  - ImageVolumes
  - NeuroVector
  - regionOfInterest
  - clustered-neurovec
  - pipelines
reference:
- title: Visualization Helpers
  desc: Plotting utilities for slices, montages, overlays, and palettes
  contents:
  - theme_neuro
  - resolve_cmap
  - scale_fill_neuro
  - annotate_orientation
  - plot_montage
  - plot_ortho
  - plot_overlay
  - mapToColors
- title: Constructors
  desc: |
    Constructors for creating and initializing various neuroimaging objects
  contents:
  - AbstractSparseNeuroVec-class
  - AFNIMetaInfo
  - ArrayLike3D-class
  - ArrayLike4D-class
  - ArrayLike5D-class
  - AxisSet-class
  - AxisSet1D-class
  - AxisSet2D-class
  - AxisSet3D-class
  - AxisSet4D-class
  - AxisSet5D-class
  - BigNeuroVec-class
  - BigNeuroVec
  - BinaryReader
  - BinaryWriter
  - BinaryWriter-class
  - ClusteredNeuroVol
  - ClusteredNeuroVec
  - ClusteredNeuroVec-class
  - DenseNeuroVec
  - DenseNeuroVol
  - FileBackedNeuroVec
  - IndexLookupVol
  - LogicalNeuroVol
  - MappedNeuroVec
  - MetaInfo-class
  - MetaInfo
  - NeuroBucket-class
  - NeuroHyperVec-class
  - NeuroHyperVec
  - NeuroObj-class
  - NeuroSlice
  - NeuroSpace
  - NeuroVec
  - NeuroVecSeq
  - NeuroVecSource
  - NeuroVecSource-class
  - NeuroVolSource
  - NeuroVol
  - NIFTIMetaInfo
  - ROICoords-class
  - ROICoords
  - ROIVec
  - ROIVol
  - SparseNeuroVec
  - SparseNeuroVol
  - TimeAxis
  - NullAxis
  - numericOrMatrix-class
- title: S4 Classes
  desc: |
    S4 classes for various neuroimaging objects
  contents:
  - BinaryReader-class
  - ColumnReader-class
  - FileBackedNeuroVec-class
  - FileFormat-class
  - FileFormat-operations
  - FileMetaInfo-class
  - FileSource-class
  - MappedNeuroVecSource-class
  - NamedAxis-class
  - NeuroSlice-class
  - NeuroSpace-class
  - NeuroVecSeq-class
  - NeuroVol-class
  - ROI-class
  - ROIVec-class
  - ROIVecWindow-class
  - ROIVol-class
  - ROIVolWindow-class
  - SparseNeuroVecSource-class
  - OrientationList2D
  - OrientationList3D
- title: Data Loading and Manipulation
  desc: |
    Methods for loading and manipulating neuroimaging data
  contents:
  - concat
  - mapf
  - vols
  - vec_from_vols
  - neuroim2
  - data_file
  - data_file_matches
  - data_reader
  - file_matches
  - read_elements
  - createNIfTIHeader
  - linear_access
  - image
  - scale
  - simulate_fmri
- title: Coordinate and Dimension Operations
  desc: |
    Methods for operating on coordinates and dimensions
  contents:
  - space
  - axes
  - spacing
  - bounds
  - centroid
  - coord_to_grid
  - coord_to_index
  - grid_to_coord
  - grid_to_index
  - grid_to_grid
  - index_to_coord
  - index_to_grid
  - dim_of
  - drop_dim
  - add_dim
  - ndim
  - voxels
  - which_dim
  - trans
  - inverse_trans
  - origin
  - perm_mat
  - strip_extension
  - deoblique
  - anatomical_axes
  - TIME
  - findAnatomy3D
  - matrixToQuatern
  - quaternToMatrix
  - affine_utils
  - orientation_utils
  - space_utils
- title: ROI and Clustering
  desc: |
    Methods for working with regions of interest and clustering
  contents:
  - partition
  - patch_set
  - split_clusters
  - centroids
  - conn_comp
  - conn_comp_3D
  - coords
  - cuboid_roi
  - num_clusters
  - slices
  - slice
  - vectors
  - values
  - spherical_roi_set
- title: Kernel and Extraction
  desc: |
    Methods for kernel operations and feature extraction
  contents:
  - Kernel
  - Kernel-class
  - embed_kernel
  - extractor3d
  - extractor4d
  - spherical_roi
  - square_roi
  - searchlight
  - searchlight_coords
  - random_searchlight
  - resampled_searchlight
  - searchlight_shape_functions
  - series_roi
  - gaussian_blur
  - guided_filter
  - bilateral_filter
  - bilateral_filter_4d
  - cgb_filter
  - cgb_make_graph
  - cgb_smooth
  - cgb_smooth_loro
  - reorient
  - clustered_searchlight
  - cluster_searchlight_series
  - spatial-filter
  - searchlight-methods
  - laplace_enhance
- title: Lookup and Mapping
  desc: |
    Methods for looking up and mapping neuroimaging data
  contents:
  - lookup
  - map_values
  - resample
  - neuro-resample
- title: Data Access and Indexing
  desc: |
    Methods for accessing and indexing neuroimaging data
  contents:
  - sub_vector
  - indices
  - length,NeuroVec-method
  - neuro-ops
- title: Scaling and Resampling
  desc: |
    Methods for splitting, scaling, processing, and resampling neuroimaging data
  contents:
  - scale_series
  - make_time_weights
  - prepare_confounds
  - resample
  - resample_to
  - neuro-downsample
  - starts_with("split_")
- title: IO
  desc: |
    Methods for input-output operations
  contents:
  - read_vec
  - read_vol
  - read_image
  - write_elements
  - write_vec
  - write_vol
  - close,BinaryReader-method
  - ColumnReader
  - header_file
  - header_file_matches
  - read_columns
  - read_header
  - read_meta_info
  - read_vol_list
  - read_hyper_vec
- title: NIfTI Extensions
  desc: |
    Classes and functions for working with NIfTI header extensions
  contents:
  - NiftiExtension
  - NiftiExtensionCodes
  - ecode_name
  - extensions
  - parse_extension
  - parse_afni_extension
  - get_afni_attribute
  - list_afni_attributes
- title: Miscellaneous
  desc: |
    Miscellaneous methods and functions
  contents:
  - starts_with("\\[")
  - starts_with("dim")
  - starts_with("drop")
  - starts_with("length")
  - starts_with("show")
  - starts_with("print")
  - starts_with("_print")
  - starts_with("as")
  - starts_with("close")
  - starts_with("plot")
  - starts_with("Arith")
  - starts_with("Compare")
  - ends_with("-method")
  - None