There is a newer version of NiBabelNiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.
Accessing NiBabel 3.2.1-foss-2020a-Python-3.8.2
To load the module for NiBabel 3.2.1-foss-2020a-Python-3.8.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load NiBabel/3.2.1-foss-2020a-Python-3.8.2
There is a GPU enabled version of this module: NiBabel 3.2.1-fosscuda-2020a-Python-3.8.2
BEAR Apps Version
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
- bz2file 0.98
- nibabel 3.2.1
For more information visit the NiBabel website.
This version of NiBabel has a direct dependency on: foss/2020a Pillow/7.0.0-GCCcore-9.3.0-Python-3.8.2 pydicom/2.1.2-GCCcore-9.3.0-Python-3.8.2 Python/3.8.2-GCCcore-9.3.0 SciPy-bundle/2020.03-foss-2020a-Python-3.8.2
These versions of NiBabel are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
Last modified on 21st December 2021