banana 0.3.5

Biomedical ANAlysis iN Arcana (Banana): biomedical analysis workflows implemented in the Arcana framework (arcana.readthedocs.io)

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

Dependencies

Core

• arcana

• nibabel

• pydicom

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

$ pip3 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)