Before we start
- Python is an open source and platform independent programming language.
- Jupyter Notebook is a great tool to code in and interact with Python.
- With the large Python community it is easy to find help on the internet.
From the scanner to our computer
- MRI can capture anatomical (structural), functional, or diffusion features.
- A number of file formats exist to store neuroimaging data.
Anatomy of a NIfTI
- NIfTI image contain a header, which describes the contents, and the data.
- The position of the NIfTI data in space is determined by the affine matrix.
- NIfTI data is a multi-dimensional array of values.
Data organization with BIDS
- BIDS is an organizational principle for neuroimaging data.
- Converting a raw MRI dataset to a BIDS-compatible dataset streamlines data processing pipelines.
Exploring open MRI datasets
- Public neuroimaging BIDS-compatible data repositories allow for pulling data easily.
- PyBIDS is a Python-based tool that allows for easy exploration of BIDS-formatted neuroimaging data.
BIDS derivatives
- BIDS Apps are containerized applications that run on BIDS-compatible datasets.