nifti2

Read / write access to NIfTI2 image format

Format described here:

Nifti2Header([binaryblock, endianness, …])

Class for NIfTI2 header

Nifti2Image(dataobj, affine[, header, …])

Class for single file NIfTI2 format image

Nifti2Pair(dataobj, affine[, header, extra, …])

Class for NIfTI2 format image, header pair

Nifti2PairHeader([binaryblock, endianness, …])

Class for NIfTI2 pair header

load(filename)

Load NIfTI2 single or pair image from filename

save(img, filename)

Save NIfTI2 single or pair to filename

Nifti2Header

class nibabel.nifti2.Nifti2Header(binaryblock=None, endianness=None, check=True, extensions=())

Bases: nibabel.nifti1.Nifti1Header

Class for NIfTI2 header

NIfTI2 is a slightly simplified variant of NIfTI1 which replaces 32-bit floats with 64-bit floats, and increases some integer widths to 32 or 64 bits.

Initialize header from binary data block and extensions

__init__(binaryblock=None, endianness=None, check=True, extensions=())

Initialize header from binary data block and extensions

classmethod default_structarr(endianness=None)

Create empty header binary block with given endianness

get_data_shape()

Get shape of data

Notes

Does not use Nifti1 freesurfer hack for large vectors described in Nifti1Header.set_data_shape()

Examples

>>> hdr = Nifti2Header()
>>> hdr.get_data_shape()
(0,)
>>> hdr.set_data_shape((1,2,3))
>>> hdr.get_data_shape()
(1, 2, 3)

Expanding number of dimensions gets default zooms

>>> hdr.get_zooms()
(1.0, 1.0, 1.0)
classmethod may_contain_header(binaryblock)
pair_magic = b'ni2'
pair_vox_offset = 0
quaternion_threshold = -6.661338147750939e-16
set_data_shape(shape)

Set shape of data

If ndims == len(shape) then we set zooms for dimensions higher than ndims to 1.0

Parameters
shapesequence

sequence of integers specifying data array shape

Notes

Does not apply nifti1 Freesurfer hack for long vectors (see Nifti1Header.set_data_shape())

single_magic = b'n+2'
single_vox_offset = 544
sizeof_hdr = 540
template_dtype = dtype([('sizeof_hdr', '<i4'), ('magic', 'S4'), ('eol_check', 'i1', (4,)), ('datatype', '<i2'), ('bitpix', '<i2'), ('dim', '<i8', (8,)), ('intent_p1', '<f8'), ('intent_p2', '<f8'), ('intent_p3', '<f8'), ('pixdim', '<f8', (8,)), ('vox_offset', '<i8'), ('scl_slope', '<f8'), ('scl_inter', '<f8'), ('cal_max', '<f8'), ('cal_min', '<f8'), ('slice_duration', '<f8'), ('toffset', '<f8'), ('slice_start', '<i8'), ('slice_end', '<i8'), ('descrip', 'S80'), ('aux_file', 'S24'), ('qform_code', '<i4'), ('sform_code', '<i4'), ('quatern_b', '<f8'), ('quatern_c', '<f8'), ('quatern_d', '<f8'), ('qoffset_x', '<f8'), ('qoffset_y', '<f8'), ('qoffset_z', '<f8'), ('srow_x', '<f8', (4,)), ('srow_y', '<f8', (4,)), ('srow_z', '<f8', (4,)), ('slice_code', '<i4'), ('xyzt_units', '<i4'), ('intent_code', '<i4'), ('intent_name', 'S16'), ('dim_info', 'u1'), ('unused_str', 'S15')])

Nifti2Image

class nibabel.nifti2.Nifti2Image(dataobj, affine, header=None, extra=None, file_map=None)

Bases: nibabel.nifti1.Nifti1Image

Class for single file NIfTI2 format image

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() and set_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

__init__(dataobj, affine, header=None, extra=None, file_map=None)

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() and set_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

header_class

alias of Nifti2Header

Nifti2Pair

class nibabel.nifti2.Nifti2Pair(dataobj, affine, header=None, extra=None, file_map=None)

Bases: nibabel.nifti1.Nifti1Pair

Class for NIfTI2 format image, header pair

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() and set_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

__init__(dataobj, affine, header=None, extra=None, file_map=None)

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() and set_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

header_class

alias of Nifti2PairHeader

Nifti2PairHeader

class nibabel.nifti2.Nifti2PairHeader(binaryblock=None, endianness=None, check=True, extensions=())

Bases: nibabel.nifti2.Nifti2Header

Class for NIfTI2 pair header

Initialize header from binary data block and extensions

__init__(binaryblock=None, endianness=None, check=True, extensions=())

Initialize header from binary data block and extensions

is_single = False

load

nibabel.nifti2.load(filename)

Load NIfTI2 single or pair image from filename

Parameters
filenamestr

filename of image to be loaded

Returns
imgNifti2Image or Nifti2Pair

nifti2 single or pair image instance

Raises
ImageFileError

if filename doesn’t look like nifti2;

IOError

if filename does not exist.

save

nibabel.nifti2.save(img, filename)

Save NIfTI2 single or pair to filename

Parameters
filenamestr

filename to which to save image