Package: neurotransform 0.1.0

neurotransform: Geometric Transforms for Neuroimaging Data

A self-contained, dependency-light library for geometric transforms in neuroimaging. Provides affine and nonlinear (warp) mappings between coordinate systems, plus volume-to-surface mapping primitives. Emphasizes correctness, elegance, and composability with a category-theoretic flavor.

Authors:Brad Buchsbaum [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
neurotransform/json (API)

# Install 'neurotransform' in R:

install.packages('neurotransform', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbuchsbaum/neurotransform/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.60 score 7 scripts 100 exports 64 dependencies

Last updated from:b63d6715b5. Checks:8 WARNING, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	255
linux-devel-x86_64	WARNING	263
source / vignettes	OK	307
linux-release-arm64	WARNING	312
linux-release-x86_64	WARNING	264
macos-release-arm64	WARNING	148
macos-release-x86_64	WARNING	470
macos-oldrel-arm64	WARNING	131
macos-oldrel-x86_64	WARNING	391
windows-devel	FAIL	146
windows-release	FAIL	148
windows-oldrel	FAIL	138
wasm-release	OK	193

Exports:adjoint 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

Dependencies:assertthat bigassertr bigparallelr bigstatsr bit cachem cli codetools cowplot cpp11 dbscan deflist digest doParallel farver fastmap ff flock foreach future future.apply generics ggplot2 globals glue gtable isoband iterators labeling lattice lifecycle listenv magrittr Matrix memoise mmap neuroim2 parallelly patchwork pillar pkgconfig ps purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RhpcBLASctl rlang rmio RNifti RNiftyReg RSpectra S7 scales stringi stringr tibble utf8 vctrs viridisLite withr

Introduction to neurotransform

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-04-12
Started: 2026-04-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get adjoint (generalized inverse)	adjoint adjoint,Affine3DMorphism-method adjoint,IdentityMorphism-method adjoint,Morphism-method adjoint,SurfToSurfMorphism-method adjoint,VolToSurfMorphism-method adjoint,Warp3DMorphism-method
Wrap an affine matrix built from components into an Affine3DMorphism	affine_from_components
Affine utilities (matrix-level and morphism helpers)	affine_utils
Create a 3D affine morphism	Affine3DMorphism
3D affine morphism	Affine3DMorphism-class
Convert RAI affine to RAS	afni_aff12_to_ras
Detect whether an affine is oblique (not cardinal axis-aligned)	afni_is_oblique
Read AFNI .aff12.1D affine matrix	afni_read_aff12
AFNI Warp and Affine Handlers	afni_warp
S4 Class Definitions for neurotransform	all_class
Generic Function Definitions	all_generic
Load ANTs composite H5 as morphism or path	ants_h5_morphism
Apply affine transformation to coordinates	apply_affine
Apply a resampling plan to a volume	apply_resampling_plan
Apply a surface resampling plan to vertex data	apply_surface_resampling
Coerce list/paths to MorphismPath	as_morphism_path
Backproject surface values into a volume (adjoint of VolToSurf sampling)	backproject_surface_to_volume
Build a 4x4 affine matrix from components	build_affine_matrix
Compose two morphisms	compose compose,Morphism,Morphism-method compose,Morphism,MorphismPath-method compose,MorphismPath,Morphism-method compose,MorphismPath,MorphismPath-method
Compose two affine transformations	compose_affines
Compute a stable hash for objects	compute_hash
Convert affine conventions between "generic" (target→source world) and "fsl" (source→target vox)	convert_affine_convention
Coordinate Convention Utilities	coordinates
Apply affines -> warp -> affines to coordinates (target -> source)	cpp_path_apply_affine_warp_affine
Apply arbitrary steps (affine/warp) to coordinates (target -> source)	cpp_path_apply_steps
Decompose a 4x4 affine matrix into components	decompose_affine_matrix
Deformation fields and Jacobian maps	deformation_field
Detect FNIRT deformation type (relative vs absolute)	detect_fnirt_def_type
Detect transform type from a file path	detect_transform_type
Dice coefficient for two images	dice_coefficient
Extract affine matrix from data	extract_affine extract_affine,ANY-method extract_affine,array-method extract_affine,DenseNeuroVec-method extract_affine,DenseNeuroVol-method extract_affine,matrix-method
Convert FLIRT matrix to internal affine	fsl_flirt_to_internal_affine
FSL Coordinate Convention Handlers	fsl_ingest
Get linear transform IO backend factory	get_linear_factory
Retrieve a warp loader by name	get_loader get_warp_loader
Get world coordinates for a grid	grid_coords
Get grid specification from volume data	grid_from_data
Extract Grid from volume or grid-like input	grid_of
Create a grid specification	grid_spec
Grid: regular coordinate grid specification	Grid-class show,Grid-method
Check if morphism has an adjoint	has_adjoint
Create an identity morphism	IdentityMorphism
Identity morphism	IdentityMorphism-class
Invert a morphism	invert invert,Affine3DMorphism-method invert,IdentityMorphism-method invert,Morphism-method invert,Warp3DMorphism-method
Invert an affine transformation	invert_affine
Check if an object is a numeric 4x4 affine matrix	is_affine_matrix
Check if an object is an Affine3DMorphism	is_affine_morphism
Check if morphism is exactly invertible	is_invertible
Check if morphism is linear (affine or identity)	is_linear_morphism
Check if a morphism path is valid	is_valid_path
Check if morphism is a warp field	is_warp_morphism
Jaccard index for two images	jaccard_index
Jacobian Computations	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
Compute Jacobian determinants	jacobian_det jacobian_det,Affine3DMorphism-method jacobian_det,IdentityMorphism-method jacobian_det,MorphismPath-method jacobian_det,Warp3DMorphism-method
Extract Jacobian determinant volume from a morphism on a grid	jacobian_det_field
Jacobian field: collection of 3x3 Jacobian matrices	det,JacobianField-method JacobianField-class length,JacobianField-method show,JacobianField-method solve,JacobianField,missing-method [,JacobianField,numeric,ANY,ANY-method [,JacobianField,numeric-method
List all registered loaders	list_loaders
Convert LPS coordinates to RAS	lps_to_ras
FreeSurfer LTA IO	lta_io
Build a resampling plan	make_resampling_plan
Check whether a surface mesh is approximately spherical	mesh_is_sphere
Set mesh radius for spherical meshes	mesh_set_radius
Morphism Constructors and Methods	morphism
Compute hash for a morphism	morphism_hash
Get the kind of a morphism	morphism_kind
Virtual base class for morphisms	Morphism-class show,Morphism-method
Morphism path (composed sequence)	MorphismPath-class
Image overlap metrics	overlap_metrics
Convert RAS coordinates to LPS	ras_to_lps
Convert scanner RAS to FreeSurfer tkRAS	ras_to_tkras
Read a 4x4 affine matrix from a text file	read_affine_matrix_txt
Simple image I/O using neuroim2	read_image
Read an affine transform file into an Affine3DMorphism	read_linear_transform
Read a series of linear transforms	read_linear_transform_array
Read transform from file into a Morphism	read_transform
Read X5 transform file	read_x5
Register a named warp loader	register_loader register_warp_loader
Resample data through a morphism	resample
High-level resampling helper	resample_to
Resample volume to new geometry	resample_volume
Resampling plans for repeated volume resampling	resampling_plan
Sample volume on surface	sample_volume_on_surface
Construct sampled points	sampled_points
Sampled points (irregular spatial reference)	SampledPoints-class show,SampledPoints-method
Sampler Classes and Resampling	sampler
Sampler: data + interpolation encapsulation	Sampler-class show,Sampler-method
Build a centered voxel-to-world affine from shape and zooms	shape_zoom_affine
Get source domain of a morphism	source_domain source_domain,Morphism-method source_of source_of,Morphism-method source_of,MorphismPath-method
Construct a surface mesh	surface_mesh
Surface Resampling Plans	surface_resampling
Build a surface resampling plan	surface_resampling_plan
Create a surface sampler	surface_sampler
Surface mesh (vertices + faces)	show,SurfaceMesh-method SurfaceMesh-class
Create a surface-to-surface morphism	SurfToSurfMorphism
Surface-to-surface morphism	SurfToSurfMorphism-class
Get target domain of a morphism	target_domain target_domain,Morphism-method target_of target_of,Morphism-method target_of,MorphismPath-method
Convert FreeSurfer tkRAS to scanner RAS	tkras_to_ras
Transform coordinates through a morphism (pullback)	transform transform,Affine3DMorphism-method transform,IdentityMorphism-method transform,MorphismPath-method transform,SurfToSurfMorphism-method transform,VolToSurfMorphism-method transform,Warp3DMorphism-method
Transform coordinates (compatibility alias)	transform_coords transform_coords,Morphism-method transform_coords,MorphismPath-method
Transform IO Helpers	transform_io
Transform Path Application	transform_path
Construct a transform file-format error condition	TransformFileError
Construct a transform IO error condition	TransformIOError
Validate a morphism path	validate_path
Create a volume-to-surface morphism	VolToSurfMorphism
Volume-to-surface morphism	VolToSurfMorphism-class
Create a volume sampler	volume_sampler
Create an in-memory dense-field warp morphism	warp_from_field
Warp Field Loader Registry	warp_loader
Create a 3D warp field morphism	Warp3DMorphism
3D warp field morphism	Warp3DMorphism-class
Write a 4x4 affine matrix to a text file	write_affine_matrix_txt
Write image using neuroim2	write_image
Write an affine transform to disk	write_linear_transform
Write a series of linear transforms	write_linear_transform_array
Write a transform to disk	write_transform
Write a warp morphism as a NIfTI vector field	write_warp_field
Write X5 transform file	write_x5
Create an X5 domain descriptor	x5_domain
X5 Transform IO	x5_io
Create an X5 transform descriptor	x5_transform