banana 0.2

Biomedical imAgiNg ANAlysis (Banana): A collection biomedical imaging analysis workflows implemented in the Arcana (arcana.readthedocs.io) framework

Biomedical imAgiNg ANAlysis (Banana): a collection of biomedical imaging analysis workflows implemented in the Arcana framework, which can be used to analyse complete study datasets in XNAT, BIDS or plain-directory repositories.

Dependencies

Core

• arcana

• nibabel

• pydicom

Both of these are available on PyPI and can be installed with:

$ pip install banana

Pipelines

Depending on which pipelines you need to run, you may need to install some or all of the following tools. Note that MRtrix3 and Dcm2niix are used for implicit format conversions so are typically required.

• MRtrix3 (https://github.com/MRtrix3/mrtrix3)

• Dcm2niix (https://github.com/rordenlab/dcm2niix)

• FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)

• Matlab (https://au.mathworks.com/products/matlab.html)

• SPM (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/)

• ANTs (https://sourceforge.net/projects/advants/)

• Freesurfer (https://surfer.nmr.mgh.harvard.edu)

• AFNI (https://afni.nimh.nih.gov)