Working with MRI

Estimated time: 70 minutes

Overview

Questions

• What kinds of MRI are there?
• How are MRI data represented digitally?
• How should I organize and structure files for neuroimaging MRI data?

Objectives

• Show common kinds of MRI imaging used in research
• Show the most common file formats for MRI
• Introduce MRI coordinate systems
• Load an MRI scan into Python and explain how the data is stored
• View and manipulate image data
• Explain what BIDS is
• Explain advantages of working with Nifti and BIDS
• Show a method to convert from DICOM to BIDS/NIfTI

Introduction

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This lesson was heavily based on existing lessons from Carpentries Incubators; namely:

1. Introduction to Working with MRI Data in Python
2. Introduction to dMRI
3. Functional Neuroimaging Analysis in Python

Until clarification over overlapping materials with all authors of these repositories has been discussed. This lesson is temporarily offline.