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  "Title": "Geometric Transforms for Neuroimaging Data",
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  "Description": "A self-contained, dependency-light library for geometric\ntransforms in neuroimaging. Provides affine and nonlinear\n(warp) mappings between coordinate systems, plus\nvolume-to-surface mapping primitives. Emphasizes correctness,\nelegance, and composability with a category-theoretic flavor.",
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    "affine_from_components",
    "Affine3DMorphism",
    "afni_aff12_to_ras",
    "afni_is_oblique",
    "afni_read_aff12",
    "ants_h5_morphism",
    "apply_affine",
    "apply_resampling_plan",
    "apply_surface_resampling",
    "as_morphism_path",
    "backproject_surface_to_volume",
    "build_affine_matrix",
    "compose",
    "compose_affines",
    "compute_hash",
    "convert_affine_convention",
    "decompose_affine_matrix",
    "deformation_field",
    "det",
    "detect_fnirt_def_type",
    "detect_transform_type",
    "dice_coefficient",
    "extract_affine",
    "fsl_flirt_to_internal_affine",
    "get_linear_factory",
    "get_loader",
    "get_warp_loader",
    "grid_coords",
    "grid_from_data",
    "grid_of",
    "grid_spec",
    "has_adjoint",
    "IdentityMorphism",
    "invert",
    "invert_affine",
    "is_affine_matrix",
    "is_affine_morphism",
    "is_invertible",
    "is_linear_morphism",
    "is_valid_path",
    "is_warp_morphism",
    "jaccard_index",
    "jacobian",
    "jacobian_det",
    "jacobian_det_field",
    "list_loaders",
    "lps_to_ras",
    "make_resampling_plan",
    "mesh_is_sphere",
    "mesh_set_radius",
    "morphism_hash",
    "morphism_kind",
    "overlap_metrics",
    "ras_to_lps",
    "ras_to_tkras",
    "read_affine_matrix_txt",
    "read_image",
    "read_linear_transform",
    "read_linear_transform_array",
    "read_transform",
    "read_x5",
    "register_loader",
    "register_warp_loader",
    "resample",
    "resample_to",
    "resample_volume",
    "sample_volume_on_surface",
    "sampled_points",
    "shape_zoom_affine",
    "show",
    "solve",
    "source_domain",
    "source_of",
    "surface_mesh",
    "surface_resampling_plan",
    "surface_sampler",
    "SurfToSurfMorphism",
    "target_domain",
    "target_of",
    "tkras_to_ras",
    "transform",
    "transform_coords",
    "transform_path",
    "TransformFileError",
    "TransformIOError",
    "validate_path",
    "VolToSurfMorphism",
    "volume_sampler",
    "warp_from_field",
    "Warp3DMorphism",
    "write_affine_matrix_txt",
    "write_image",
    "write_linear_transform",
    "write_linear_transform_array",
    "write_transform",
    "write_warp_field",
    "write_x5",
    "x5_domain",
    "x5_transform"
  ],
  "_help": [
    {
      "page": "adjoint",
      "title": "Get adjoint (generalized inverse)",
      "topics": [
        "adjoint",
        "adjoint,Affine3DMorphism-method",
        "adjoint,IdentityMorphism-method",
        "adjoint,Morphism-method",
        "adjoint,SurfToSurfMorphism-method",
        "adjoint,VolToSurfMorphism-method",
        "adjoint,Warp3DMorphism-method"
      ]
    },
    {
      "page": "affine_from_components",
      "title": "Wrap an affine matrix built from components into an Affine3DMorphism",
      "topics": [
        "affine_from_components"
      ]
    },
    {
      "page": "affine_utils",
      "title": "Affine utilities (matrix-level and morphism helpers)",
      "topics": [
        "affine_utils"
      ]
    },
    {
      "page": "Affine3DMorphism",
      "title": "Create a 3D affine morphism",
      "topics": [
        "Affine3DMorphism"
      ]
    },
    {
      "page": "Affine3DMorphism-class",
      "title": "3D affine morphism",
      "topics": [
        "Affine3DMorphism-class"
      ]
    },
    {
      "page": "afni_aff12_to_ras",
      "title": "Convert RAI affine to RAS",
      "topics": [
        "afni_aff12_to_ras"
      ]
    },
    {
      "page": "afni_is_oblique",
      "title": "Detect whether an affine is oblique (not cardinal axis-aligned)",
      "topics": [
        "afni_is_oblique"
      ]
    },
    {
      "page": "afni_read_aff12",
      "title": "Read AFNI .aff12.1D affine matrix",
      "topics": [
        "afni_read_aff12"
      ]
    },
    {
      "page": "afni_warp",
      "title": "AFNI Warp and Affine Handlers",
      "topics": [
        "afni_warp"
      ]
    },
    {
      "page": "all_class",
      "title": "S4 Class Definitions for neurotransform",
      "topics": [
        "all_class"
      ]
    },
    {
      "page": "all_generic",
      "title": "Generic Function Definitions",
      "topics": [
        "all_generic"
      ]
    },
    {
      "page": "ants_h5_morphism",
      "title": "Load ANTs composite H5 as morphism or path",
      "topics": [
        "ants_h5_morphism"
      ]
    },
    {
      "page": "apply_affine",
      "title": "Apply affine transformation to coordinates",
      "topics": [
        "apply_affine"
      ]
    },
    {
      "page": "apply_resampling_plan",
      "title": "Apply a resampling plan to a volume",
      "topics": [
        "apply_resampling_plan"
      ]
    },
    {
      "page": "apply_surface_resampling",
      "title": "Apply a surface resampling plan to vertex data",
      "topics": [
        "apply_surface_resampling"
      ]
    },
    {
      "page": "as_morphism_path",
      "title": "Coerce list/paths to MorphismPath",
      "topics": [
        "as_morphism_path"
      ]
    },
    {
      "page": "backproject_surface_to_volume",
      "title": "Backproject surface values into a volume (adjoint of VolToSurf sampling)",
      "topics": [
        "backproject_surface_to_volume"
      ]
    },
    {
      "page": "build_affine_matrix",
      "title": "Build a 4x4 affine matrix from components",
      "topics": [
        "build_affine_matrix"
      ]
    },
    {
      "page": "compose",
      "title": "Compose two morphisms",
      "topics": [
        "compose",
        "compose,Morphism,Morphism-method",
        "compose,Morphism,MorphismPath-method",
        "compose,MorphismPath,Morphism-method",
        "compose,MorphismPath,MorphismPath-method"
      ]
    },
    {
      "page": "compose_affines",
      "title": "Compose two affine transformations",
      "topics": [
        "compose_affines"
      ]
    },
    {
      "page": "compute_hash",
      "title": "Compute a stable hash for objects",
      "topics": [
        "compute_hash"
      ]
    },
    {
      "page": "convert_affine_convention",
      "title": "Convert affine conventions between \"generic\" (target→source world) and \"fsl\" (source→target vox)",
      "topics": [
        "convert_affine_convention"
      ]
    },
    {
      "page": "coordinates",
      "title": "Coordinate Convention Utilities",
      "topics": [
        "coordinates"
      ]
    },
    {
      "page": "cpp_path_apply_affine_warp_affine",
      "title": "Apply affines -> warp -> affines to coordinates (target -> source)",
      "topics": [
        "cpp_path_apply_affine_warp_affine"
      ]
    },
    {
      "page": "cpp_path_apply_steps",
      "title": "Apply arbitrary steps (affine/warp) to coordinates (target -> source)",
      "topics": [
        "cpp_path_apply_steps"
      ]
    },
    {
      "page": "decompose_affine_matrix",
      "title": "Decompose a 4x4 affine matrix into components",
      "topics": [
        "decompose_affine_matrix"
      ]
    },
    {
      "page": "deformation_field",
      "title": "Deformation fields and Jacobian maps",
      "topics": [
        "deformation_field"
      ]
    },
    {
      "page": "detect_fnirt_def_type",
      "title": "Detect FNIRT deformation type (relative vs absolute)",
      "topics": [
        "detect_fnirt_def_type"
      ]
    },
    {
      "page": "detect_transform_type",
      "title": "Detect transform type from a file path",
      "topics": [
        "detect_transform_type"
      ]
    },
    {
      "page": "dice_coefficient",
      "title": "Dice coefficient for two images",
      "topics": [
        "dice_coefficient"
      ]
    },
    {
      "page": "extract_affine",
      "title": "Extract affine matrix from data",
      "topics": [
        "extract_affine",
        "extract_affine,ANY-method",
        "extract_affine,array-method",
        "extract_affine,DenseNeuroVec-method",
        "extract_affine,DenseNeuroVol-method",
        "extract_affine,matrix-method"
      ]
    },
    {
      "page": "fsl_flirt_to_internal_affine",
      "title": "Convert FLIRT matrix to internal affine",
      "topics": [
        "fsl_flirt_to_internal_affine"
      ]
    },
    {
      "page": "fsl_ingest",
      "title": "FSL Coordinate Convention Handlers",
      "topics": [
        "fsl_ingest"
      ]
    },
    {
      "page": "get_linear_factory",
      "title": "Get linear transform IO backend factory",
      "topics": [
        "get_linear_factory"
      ]
    },
    {
      "page": "get_loader",
      "title": "Retrieve a warp loader by name",
      "topics": [
        "get_loader",
        "get_warp_loader"
      ]
    },
    {
      "page": "grid_coords",
      "title": "Get world coordinates for a grid",
      "topics": [
        "grid_coords"
      ]
    },
    {
      "page": "grid_from_data",
      "title": "Get grid specification from volume data",
      "topics": [
        "grid_from_data"
      ]
    },
    {
      "page": "grid_of",
      "title": "Extract Grid from volume or grid-like input",
      "topics": [
        "grid_of"
      ]
    },
    {
      "page": "grid_spec",
      "title": "Create a grid specification",
      "topics": [
        "grid_spec"
      ]
    },
    {
      "page": "Grid-class",
      "title": "Grid: regular coordinate grid specification",
      "topics": [
        "Grid-class",
        "show,Grid-method"
      ]
    },
    {
      "page": "has_adjoint",
      "title": "Check if morphism has an adjoint",
      "topics": [
        "has_adjoint"
      ]
    },
    {
      "page": "IdentityMorphism",
      "title": "Create an identity morphism",
      "topics": [
        "IdentityMorphism"
      ]
    },
    {
      "page": "IdentityMorphism-class",
      "title": "Identity morphism",
      "topics": [
        "IdentityMorphism-class"
      ]
    },
    {
      "page": "invert",
      "title": "Invert a morphism",
      "topics": [
        "invert",
        "invert,Affine3DMorphism-method",
        "invert,IdentityMorphism-method",
        "invert,Morphism-method",
        "invert,Warp3DMorphism-method"
      ]
    },
    {
      "page": "invert_affine",
      "title": "Invert an affine transformation",
      "topics": [
        "invert_affine"
      ]
    },
    {
      "page": "is_affine_matrix",
      "title": "Check if an object is a numeric 4x4 affine matrix",
      "topics": [
        "is_affine_matrix"
      ]
    },
    {
      "page": "is_affine_morphism",
      "title": "Check if an object is an Affine3DMorphism",
      "topics": [
        "is_affine_morphism"
      ]
    },
    {
      "page": "is_invertible",
      "title": "Check if morphism is exactly invertible",
      "topics": [
        "is_invertible"
      ]
    },
    {
      "page": "is_linear_morphism",
      "title": "Check if morphism is linear (affine or identity)",
      "topics": [
        "is_linear_morphism"
      ]
    },
    {
      "page": "is_valid_path",
      "title": "Check if a morphism path is valid",
      "topics": [
        "is_valid_path"
      ]
    },
    {
      "page": "is_warp_morphism",
      "title": "Check if morphism is a warp field",
      "topics": [
        "is_warp_morphism"
      ]
    },
    {
      "page": "jaccard_index",
      "title": "Jaccard index for two images",
      "topics": [
        "jaccard_index"
      ]
    },
    {
      "page": "jacobian",
      "title": "Jacobian Computations",
      "topics": [
        "jacobian",
        "jacobian,Affine3DMorphism,ANY-method",
        "jacobian,DeformationField,missing-method",
        "jacobian,IdentityMorphism,ANY-method",
        "jacobian,MorphismPath,ANY-method",
        "jacobian,SurfToSurfMorphism,ANY-method",
        "jacobian,VolToSurfMorphism,ANY-method",
        "jacobian,Warp3DMorphism,ANY-method"
      ]
    },
    {
      "page": "jacobian_det",
      "title": "Compute Jacobian determinants",
      "topics": [
        "jacobian_det",
        "jacobian_det,Affine3DMorphism-method",
        "jacobian_det,IdentityMorphism-method",
        "jacobian_det,MorphismPath-method",
        "jacobian_det,Warp3DMorphism-method"
      ]
    },
    {
      "page": "jacobian_det_field",
      "title": "Extract Jacobian determinant volume from a morphism on a grid",
      "topics": [
        "jacobian_det_field"
      ]
    },
    {
      "page": "JacobianField-class",
      "title": "Jacobian field: collection of 3x3 Jacobian matrices",
      "topics": [
        "det,JacobianField-method",
        "JacobianField-class",
        "length,JacobianField-method",
        "show,JacobianField-method",
        "solve,JacobianField,missing-method",
        "[,JacobianField,numeric,ANY,ANY-method",
        "[,JacobianField,numeric-method"
      ]
    },
    {
      "page": "list_loaders",
      "title": "List all registered loaders",
      "topics": [
        "list_loaders"
      ]
    },
    {
      "page": "lps_to_ras",
      "title": "Convert LPS coordinates to RAS",
      "topics": [
        "lps_to_ras"
      ]
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    {
      "page": "lta_io",
      "title": "FreeSurfer LTA IO",
      "topics": [
        "lta_io"
      ]
    },
    {
      "page": "make_resampling_plan",
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      "topics": [
        "make_resampling_plan"
      ]
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    {
      "page": "mesh_is_sphere",
      "title": "Check whether a surface mesh is approximately spherical",
      "topics": [
        "mesh_is_sphere"
      ]
    },
    {
      "page": "mesh_set_radius",
      "title": "Set mesh radius for spherical meshes",
      "topics": [
        "mesh_set_radius"
      ]
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      "page": "morphism",
      "title": "Morphism Constructors and Methods",
      "topics": [
        "morphism"
      ]
    },
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      "page": "morphism_hash",
      "title": "Compute hash for a morphism",
      "topics": [
        "morphism_hash"
      ]
    },
    {
      "page": "morphism_kind",
      "title": "Get the kind of a morphism",
      "topics": [
        "morphism_kind"
      ]
    },
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      "page": "Morphism-class",
      "title": "Virtual base class for morphisms",
      "topics": [
        "Morphism-class",
        "show,Morphism-method"
      ]
    },
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      "page": "MorphismPath-class",
      "title": "Morphism path (composed sequence)",
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        "MorphismPath-class"
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    },
    {
      "page": "overlap_metrics",
      "title": "Image overlap metrics",
      "topics": [
        "overlap_metrics"
      ]
    },
    {
      "page": "ras_to_lps",
      "title": "Convert RAS coordinates to LPS",
      "topics": [
        "ras_to_lps"
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      "page": "ras_to_tkras",
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      "topics": [
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      "page": "read_affine_matrix_txt",
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        "read_affine_matrix_txt"
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    {
      "page": "read_image",
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      "page": "read_linear_transform",
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      "topics": [
        "read_linear_transform"
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      "page": "read_linear_transform_array",
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      "topics": [
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      "page": "read_transform",
      "title": "Read transform from file into a Morphism",
      "topics": [
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    {
      "page": "read_x5",
      "title": "Read X5 transform file",
      "topics": [
        "read_x5"
      ]
    },
    {
      "page": "register_loader",
      "title": "Register a named warp loader",
      "topics": [
        "register_loader",
        "register_warp_loader"
      ]
    },
    {
      "page": "resample",
      "title": "Resample data through a morphism",
      "topics": [
        "resample"
      ]
    },
    {
      "page": "resample_to",
      "title": "High-level resampling helper",
      "topics": [
        "resample_to"
      ]
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    {
      "page": "resample_volume",
      "title": "Resample volume to new geometry",
      "topics": [
        "resample_volume"
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    },
    {
      "page": "resampling_plan",
      "title": "Resampling plans for repeated volume resampling",
      "topics": [
        "resampling_plan"
      ]
    },
    {
      "page": "sample_volume_on_surface",
      "title": "Sample volume on surface",
      "topics": [
        "sample_volume_on_surface"
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    },
    {
      "page": "sampled_points",
      "title": "Construct sampled points",
      "topics": [
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    },
    {
      "page": "SampledPoints-class",
      "title": "Sampled points (irregular spatial reference)",
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        "SampledPoints-class",
        "show,SampledPoints-method"
      ]
    },
    {
      "page": "sampler",
      "title": "Sampler Classes and Resampling",
      "topics": [
        "sampler"
      ]
    },
    {
      "page": "Sampler-class",
      "title": "Sampler: data + interpolation encapsulation",
      "topics": [
        "Sampler-class",
        "show,Sampler-method"
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    },
    {
      "page": "shape_zoom_affine",
      "title": "Build a centered voxel-to-world affine from shape and zooms",
      "topics": [
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    },
    {
      "page": "source_of",
      "title": "Get source domain of a morphism",
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        "source_domain,Morphism-method",
        "source_of",
        "source_of,Morphism-method",
        "source_of,MorphismPath-method"
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    {
      "page": "surface_mesh",
      "title": "Construct a surface mesh",
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    },
    {
      "page": "surface_resampling",
      "title": "Surface Resampling Plans",
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      "page": "surface_resampling_plan",
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    {
      "page": "surface_sampler",
      "title": "Create a surface sampler",
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      "page": "SurfaceMesh-class",
      "title": "Surface mesh (vertices + faces)",
      "topics": [
        "show,SurfaceMesh-method",
        "SurfaceMesh-class"
      ]
    },
    {
      "page": "SurfToSurfMorphism",
      "title": "Create a surface-to-surface morphism",
      "topics": [
        "SurfToSurfMorphism"
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      "page": "SurfToSurfMorphism-class",
      "title": "Surface-to-surface morphism",
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      "page": "target_of",
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        "target_domain,Morphism-method",
        "target_of",
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      "page": "tkras_to_ras",
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    {
      "page": "transform",
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        "transform,Affine3DMorphism-method",
        "transform,IdentityMorphism-method",
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        "transform_coords,MorphismPath-method"
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      "page": "transform_path",
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    },
    {
      "page": "TransformFileError",
      "title": "Construct a transform file-format error condition",
      "topics": [
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    },
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      "title": "Construct a transform IO error condition",
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      "page": "VolToSurfMorphism",
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      "page": "VolToSurfMorphism-class",
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      "title": "Warp Field Loader Registry",
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      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to neurotransform",
      "author": "Brad Buchsbaum",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Design Philosophy",
        "Core Concepts",
        "What is a Morphism?",
        "The Morphism Hierarchy",
        "Quick Start",
        "Creating Morphisms",
        "Transforming Coordinates",
        "Composing Transforms",
        "Inverting Transforms",
        "Working with Neuroimaging Tools",
        "ANTs Transforms",
        "FSL Transforms",
        "AFNI Transforms",
        "FreeSurfer Coordinates",
        "Resampling Data",
        "Volume Samplers",
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        "Coordinate Conventions",
        "Affine Utilities",
        "Building Affine Matrices",
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        "Common Workflows",
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        "Workflow 2: Transform ROI Coordinates",
        "Workflow 3: Chain Multiple Transforms",
        "Performance Tips",
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      "created": "2026-04-12 23:16:20",
      "modified": "2026-04-12 23:16:20",
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