Banana
Biomedical 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
Both 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)