Package: ciftier 0.1.0

ciftier: Read and Write CIFTI-2 Neuroimaging Files

Pure R implementation of CIFTI-2 format I/O for grayordinate neuroimaging data. Reads and writes dense timeseries (.dtseries.nii), dense scalars (.dscalar.nii), and dense labels (.dlabel.nii) files without requiring external tools such as Connectome Workbench. Provides S4 classes mirroring the CIFTI-2 XML schema, user-friendly axis abstractions, and optional integration with 'neuroim2' and 'neurosurf' for spatially-aware brain imaging objects.

Authors:Bradley R Buchsbaum [aut, cre, cph]

ciftier_0.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ciftier/json (API)

# Install 'ciftier' in R:
install.packages('ciftier', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

Conda:

2.00 score 45 exports 5 dependencies

Last updated from:dc2f46b925. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK208
source / vignettesOK263
linux-release-x86_64OK167
macos-release-arm64OK87
macos-oldrel-arm64OK87
windows-develOK94
windows-releaseOK99
windows-oldrelOK95
wasm-releaseOK167

Exports:as_bilat_surface_vectoras_neuro_surfaceas_neuro_vecas_neuro_volaxes_to_headerbrain_model_from_maskbrain_model_from_surfacebrain_modelsbuild_cifti_xmlcifti_datacifti_from_datacifti_headerCIFTI_INDEX_TYPEScifti_intentCIFTI_INTENTSCIFTI_MODEL_TYPESCIFTI_SERIES_UNITSCIFTI_STRUCTURESCiftiImagecol_axisdconndlabeldpconndscalardtseriesextract_structureheader_to_axesiter_structuresnamed_mapsparcels_from_brain_modelsparse_cifti_xmlpconnpcseriespdconnplabelpscalarptseriesread_ciftirow_axisshowto_cifti_indexto_cifti_structure_nameto_r_indexvolume_infowrite_cifti

Dependencies:cliRcpprlangRNiftixml2

Readme and manuals

Help Manual

Help pageTopics
Extract Bilateral Surface Data as a neurosurf Objectas_bilat_surface_vector
Extract Surface Data as a neurosurf Objectas_neuro_surface
Extract All Subcortical Volume Data as a neuroim2 Objectas_neuro_vec
Extract Volume Data as a neuroim2 Objectas_neuro_vol
Convert Axis Objects Back to CiftiHeaderaxes_to_header
Create a BrainModelAxis from a Maskbrain_model_from_mask
Create a BrainModelAxis from Surface Vertex Indicesbrain_model_from_surface
Get Brain Models from an Objectbrain_models
BrainModelAxis Class==,BrainModelAxis,BrainModelAxis-method BrainModelAxis-class c,BrainModelAxis-method iter_structures,BrainModelAxis-method length,BrainModelAxis-method show,BrainModelAxis-method [,BrainModelAxis,logical,missing-method [,BrainModelAxis,numeric,missing-method
Build CIFTI-2 XML from Headerbuild_cifti_xml
Get the Data Matrixcifti_data
Build a CiftiImage from Spatial Data Objectscifti_from_data
Get the CIFTI Headercifti_header
CIFTI-2 Index TypesCIFTI_INDEX_TYPES
Get the NIfTI Intent Codecifti_intent
CIFTI-2 NIfTI Intent CodesCIFTI_INTENTS
CIFTI-2 Brain Model TypesCIFTI_MODEL_TYPES
CIFTI-2 Series Unit TypesCIFTI_SERIES_UNITS
CIFTI-2 Brain Structure NamesCIFTI_STRUCTURES
CiftiAxis Virtual Base ClassCiftiAxis-class
CiftiBrainModel ClassCiftiBrainModel-class
CiftiHeader ClassCiftiHeader-class
Create a CiftiImageCiftiImage
CiftiImage Classbrain_models,CiftiImage-method CiftiImage-class cifti_data,CiftiImage-method cifti_header,CiftiImage-method cifti_intent,CiftiImage-method col_axis,CiftiImage-method dim,CiftiImage-method extract_structure,CiftiImage,character-method named_maps,CiftiImage-method row_axis,CiftiImage-method show,CiftiImage-method volume_info,CiftiImage-method [,CiftiImage,ANY,ANY-method
CiftiLabel ClassCiftiLabel-class
CiftiLabelTable ClassCiftiLabelTable-class
CiftiMatrix ClassCiftiMatrix-class
CiftiMatrixIndicesMap ClassCiftiMatrixIndicesMap-class
CiftiNamedMap ClassCiftiNamedMap-class
CiftiParcel ClassCiftiParcel-class
CiftiSurface ClassCiftiSurface-class
CiftiVolume ClassCiftiVolume-class
Get the Column Axis of a CIFTI Objectcol_axis
Create a Dense Connectivity CIFTI Imagedconn
Create a Dense Label CIFTI Imagedlabel
Create a Dense-to-Parcel Connectivity CIFTI Imagedpconn
Create a Dense Scalar CIFTI Imagedscalar
Create a Dense Timeseries CIFTI Imagedtseries
Extract Data for a Single Brain Structureextract_structure
Convert CiftiHeader to Axis Objectsheader_to_axes
Iterate Over Brain Structuresiter_structures
LabelAxis ClassLabelAxis-class length,LabelAxis-method show,LabelAxis-method [,LabelAxis,numeric,missing-method
Get Named Maps from an Objectnamed_maps
Create a ParcelsAxis from Brain Modelsparcels_from_brain_models
ParcelsAxis Classiter_structures,ParcelsAxis-method length,ParcelsAxis-method ParcelsAxis-class show,ParcelsAxis-method [,ParcelsAxis,numeric,missing-method
Parse CIFTI-2 XML Headerparse_cifti_xml
Create a Parcel Connectivity CIFTI Imagepconn
Create a Parcel Series CIFTI Imagepcseries
Create a Parcel-to-Dense Connectivity CIFTI Imagepdconn
Create a Parcel Label CIFTI Imageplabel
Create a Parcel Scalar CIFTI Imagepscalar
Create a Parcel Timeseries CIFTI Imageptseries
Read a CIFTI-2 Fileread_cifti
Get the Row Axis of a CIFTI Objectrow_axis
ScalarAxis Class==,ScalarAxis,ScalarAxis-method c,ScalarAxis-method length,ScalarAxis-method ScalarAxis-class show,ScalarAxis-method [,ScalarAxis,numeric,missing-method
SeriesAxis Class==,SeriesAxis,SeriesAxis-method c,SeriesAxis-method length,SeriesAxis-method SeriesAxis-class show,SeriesAxis-method [,SeriesAxis,numeric,missing-method
Convert 1-based R Index to 0-based CIFTI Indexto_cifti_index
Normalize a Brain Structure Name to CIFTI Conventionto_cifti_structure_name
Convert 0-based CIFTI Index to 1-based R Indexto_r_index
Get Volume Informationvolume_info
Write a CIFTI-2 Filewrite_cifti