NiBabel 2016

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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. [¹]

Installed version(s)

This version is installed and currently available

on environment hpc-env/6.4:

  • NiBabel/2.2.1-intel-2018a-Python-3.6.3

on environment hpc-env/8.3:

  • NiBabel/3.2.0-foss-2019b-Python-3.7.4

Loading / Using NiBabel

To load the desired version of the module, use the command, e.g.

module load hpc-env/8.3
module load NiBabel

Always remember: this command is case sensitive!

NiBabel comes with some binary files which can be used independently outside of Python. Since the available executables differ from version to version, it would be best to load the module of your choice and type in the following to list the available commands:


To learn more about how NiBabel is used inside of Python as a module, please consult the developers guide on [getting started]


The full documentation can be found here.