Class NiftiHeader

Constructors

constructor

Properties

auxilaryFile calibrationMax calibrationMin dataIntercept dataSlope datatypeCode description dimInfo dims intentCode intentName intentP1 intentP2 intentP3 littleEndian magic numBitsPerVoxel pixDims qFormCode qOffsetX qOffsetY qOffsetZ quaternB quaternC quaternD sFormCode sliceCode sliceDuration sliceEnd sliceStart sRowX sRowY sRowZ timeOffset voxOffset xyztUnits

Accessors

spatialUnits temporalUnits

Methods

computeAffine formatHeader getDatatypeDisplayName getNiftiVersion getNiftiVersionDisplayName getQFormDisplayName getSFormDisplayName getSpatialUnitsDisplayName getTemporalUnitsDisplayName isValid serializeNifti1 serializeNifti2 parse parseNifti1 parseNifti2 peekVersion

Constructors

constructor

Properties

auxilaryFile

auxilaryFile: string = ''

Auxiliary filename (24 chars max)

calibrationMax

calibrationMax: number = 0.0

Calibration display range

calibrationMin

calibrationMin: number = 0.0

Calibration display range

dataIntercept

dataIntercept: number = 0

Data scaling factor: output = input * scl_slope + scl_inter

dataSlope

dataSlope: number = 1.0

Data scaling factor: output = input * scl_slope + scl_inter

datatypeCode

datatypeCode: number = 0

Data type code defining data format

See

DataTypeCode enum

description

description: string = ''

Free-form data description (80 chars max)

dimInfo

dimInfo: number = 0

MRI slice ordering information

dims

dims: DimensionArray = ...

Array representing dimensions of a NIfTI volume.

Represents the dimensions of a NIfTI volume as an 8-element array where:

  • Index 0: Number of dimensions (rank) of the dataset (1-7)
  • Index 1: Size of dimension 1 (usually x dimension)
  • Index 2: Size of dimension 2 (usually y dimension)
  • Index 3: Size of dimension 3 (usually z dimension)
  • Index 4: Size of dimension 4 (usually time points)
  • Index 5-7: Sizes of optional additional dimensions

Example

// 3D volume of size 256x256x128
const dims: DimensionArray = [3, 256, 256, 128, 1, 1, 1, 1];

// 4D volume (fMRI) with 30 time points
const timeSeries: DimensionArray = [4, 64, 64, 32, 30, 1, 1, 1];

intentCode

intentCode: number = 0

Specifies the intended meaning of the data

intentName

intentName: string = ''

Name or meaning of the data (16 chars max)

intentP1

intentP1: number = 0

Intent parameters - Used to store statistical parameters Meaning depends on intent_code

intentP2

intentP2: number = 0

intentP3

intentP3: number = 0

littleEndian

littleEndian: boolean = false

File encoding.

magic

magic: string = 'ni1'

NIFTI format identifier. Invalid if anything other than "ni1" | "n+1" | "ni2" | "n+2"

numBitsPerVoxel

numBitsPerVoxel: number = 0

Number of bits per voxel

pixDims

pixDims: DimensionArray = ...

Pixel dimensions:

  • Index 0: (not used for pixdims)
  • Index 1: Pixel width in dimension 1 (usually x dimension)
  • Index 2: Pixel width in dimension 2 (usually y dimension)
  • Index 3: Pixel width in dimension 3 (usually z dimension)
  • Index 4: Time step duration (TR) for dimension 4
  • Index 5-7: Step sizes for optional additional dimensions

qFormCode

qFormCode: number = 0

Transform codes defining spatial orientation

qOffsetX

qOffsetX: number = 0.0

qOffsetY

qOffsetY: number = 0.0

qOffsetZ

qOffsetZ: number = 0.0

quaternB

quaternB: number = 0.0

Quaternion parameters for spatial transform

quaternC

quaternC: number = 0.0

quaternD

quaternD: number = 0.0

sFormCode

sFormCode: number = 0

Transform codes defining spatial orientation

sliceCode

sliceCode: number = 0

Slice timing order code

sliceDuration

sliceDuration: number = 0

Time for 1 slice in seconds

sliceEnd

sliceEnd: number = 0

Last slice index

sliceStart

sliceStart: number = 0

First slice index

sRowX

sRowX: [number, number, number, number] = ...

S-Form parameters for spatial transform

sRowY

sRowY: [number, number, number, number] = ...

sRowZ

sRowZ: [number, number, number, number] = ...

timeOffset

timeOffset: number = 0

Time axis shift

voxOffset

voxOffset: number = 0

Byte offset into the .nii file where pixel data starts

xyztUnits

xyztUnits: number = 0

Units of pixdim[1..4] Bits 0-2: spatial units Bits 3-5: temporal units

Accessors

spatialUnits

  • get spatialUnits(): number

  • Gets the spatial units code from the combined units value

    Returns number

    Spatial units code extracted using SPATIAL_UNITS_MASK

  • set spatialUnits(value: number): void

  • Sets the spatial units while preserving temporal units

    Parameters

    • value: number

      New spatial units code to set

    Returns void

temporalUnits

  • get temporalUnits(): number

  • Gets the temporal units code from the combined units value

    Returns number

    Temporal units code extracted using TEMPORAL_UNITS_MASK

  • set temporalUnits(value: number): void

  • Sets the temporal units while preserving spatial units

    Parameters

    • value: number

      New temporal units code to set

    Returns void

Methods

computeAffine

formatHeader

  • formatHeader(): string

  • Formats header information in a simple markdown-style format

    Returns string

getDatatypeDisplayName

  • getDatatypeDisplayName(): string

  • Get the data type as a human readable string

    Returns string

getNiftiVersion

getNiftiVersionDisplayName

  • getNiftiVersionDisplayName(): string

  • Gets human-readable name for NIFTI version

    Returns string

getQFormDisplayName

  • getQFormDisplayName(): string

  • Get the QForm transform code as a human readable string

    Returns string

getSFormDisplayName

  • getSFormDisplayName(): string

  • Get the SForm transform code as a human readable string

    Returns string

getSpatialUnitsDisplayName

  • getSpatialUnitsDisplayName(): string

  • Gets a human-readable string representation of the spatial units

    Returns string

    Display name corresponding to the current spatial units code

getTemporalUnitsDisplayName

  • getTemporalUnitsDisplayName(): string

  • Gets a human-readable string representation of the temporal units

    Returns string

    Display name corresponding to the current temporal units code

isValid

serializeNifti1

  • serializeNifti1(): Uint8Array<ArrayBufferLike>

  • Serializes the NIFTI-1 header data into a binary format. Creates a new typed array and copies all header fields according to the NIFTI-1 specification, handling endianness conversion.

    Returns Uint8Array<ArrayBufferLike>

    Uint8Array containing the complete NIFTI-1 header (348 bytes)

serializeNifti2

  • serializeNifti2(): ArrayBuffer

  • Serializes the NIFTI-2 header data into a binary format. Creates a new typed array and copies all header fields according to the NIFTI-2 specification, handling endianness conversion.

    Returns ArrayBuffer

    Uint8Array containing the complete NIFTI-1 header (540 bytes)

Staticparse

  • parse(
        view: DataView<ArrayBufferLike>,
        peekInfo: NiftiHeaderPeekInfo,
    ): NiftiHeader

  • Parses a NIFTI header from a DataView based on header version information.

    Parameters

    • view: DataView<ArrayBufferLike>

      DataView containing the NIFTI header data

    • peekInfo: NiftiHeaderPeekInfo

      Header version and endianness information from peekVersion

    Returns NiftiHeader

    Parsed NiftiHeader object

StaticparseNifti1

  • parseNifti1(
        view: DataView<ArrayBufferLike>,
        littleEndian?: boolean,
    ): NiftiHeader

  • Parses a NIFTI-1 format header from a DataView.

    Parameters

    • view: DataView<ArrayBufferLike>

      DataView containing the NIFTI header data

    • OptionallittleEndian: boolean

      Whether to read values as little-endian (from peekNiftiHeader)

    Returns NiftiHeader

    A NiftiHeader object containing the parsed header fields

    See

    https://nifti.nimh.nih.gov/nifti-1/ for header specification

StaticparseNifti2

  • parseNifti2(
        view: DataView<ArrayBufferLike>,
        littleEndian?: boolean,
    ): NiftiHeader

  • Parses a NIFTI-2 format header from a DataView.

    Parameters

    • view: DataView<ArrayBufferLike>

      DataView containing the NIFTI header data

    • OptionallittleEndian: boolean

      Whether to read values as little-endian (from peekVersion)

    Returns NiftiHeader

    A NiftiHeader object containing the parsed header fields

    See

    https://nifti.nimh.nih.gov/nifti-2/ for header specification

StaticpeekVersion

  • peekVersion(view: DataView<ArrayBufferLike>): undefined | NiftiHeaderPeekInfo

  • Peek at first 4 bytes of header to determine nifti version and endianness. Returns undefined if not a nifti header.

    Parameters

    • view: DataView<ArrayBufferLike>

    Returns undefined | NiftiHeaderPeekInfo

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