`nibabel`¶

Read / write access to some common neuroimaging file formats

This package provides read +/- write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD, MGH and ECAT as well as Philips PAR/REC. We can read and write FreeSurfer geometry, annotation and morphometry files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays.

Website¶

Current documentation on nibabel can always be found at the NIPY nibabel website.

Mailing Lists¶

Please send any questions or suggestions to the neuroimaging mailing list.

Code¶

Install nibabel with:

pip install nibabel

License¶

Nibabel is licensed under the terms of the MIT license. Some code included with nibabel is licensed under the BSD license. Please see the COPYING file in the nibabel distribution.

Citing nibabel¶

Please see the available releases for the release of nibabel that you are using. Recent releases have a Zenodo Digital Object Identifier badge at the top of the release notes. Click on the badge for more information.

Quickstart¶

import nibabel as nib

img1 = nib.load('my_file.nii')
img2 = nib.load('other_file.nii.gz')
img3 = nib.load('spm_file.img')

data = img1.get_fdata()
affine = img1.affine

print(img1)

nib.save(img1, 'my_file_copy.nii.gz')

new_image = nib.Nifti1Image(data, affine)
nib.save(new_image, 'new_image.nii.gz')

For more detailed information see the NiBabel Manual.

`bench`([label, verbose, extra_argv])	Run benchmarks for nibabel using pytest
`get_info`()
`test`([label, verbose, extra_argv, doctests, ...])	Run tests for nibabel using pytest

bench¶

nibabel.bench(label=None, verbose=1, extra_argv=None)¶

Run benchmarks for nibabel using pytest

The protocol mimics the numpy.testing.NoseTester.bench(). Not all features are currently implemented.

Parameters:

labelNone: Unused.
verbose: int, optional: Verbosity value for test outputs. Positive values increase verbosity, and negative values decrease it. Default is 1.
extra_argvlist, optional: List with any extra arguments to pass to pytest.

Returns:

codeExitCode: Returns the result of running the tests as a pytest.ExitCode enum

get_info¶

nibabel.get_info()¶

test¶

nibabel.test(label=None, verbose=1, extra_argv=None, doctests=False, coverage=False, raise_warnings=None, timer=False)¶

Run tests for nibabel using pytest

The protocol mimics the numpy.testing.NoseTester.test(). Not all features are currently implemented.