This lesson is still being designed and assembled (Pre-Alpha version)

Lesson Title

FIXME: sMRI analysis in Neuroimaging


Attendees must have some base familiarity with Python and NIfTI images in order to comfortably progress through the lesson


Setup Download files required for the lesson
00:00 1. Course Overview How are structural MR imaging analyses performed?
00:30 2. Introduction to structural MR image modalities How is structural MR image acquired?
What anatomical features do different modalities capture?
01:00 3. Image preprocessing with smriprep (Part 1: image clean-up) What are the sources of noise and artifacts in MR images?
How do we extract/mask the brain?
01:30 4. Image preprocessing with smriprep (Part 2: spatial normalization) What is spatial normalization?
What are ‘templates’, ‘spaces’, ‘atlases’?
02:00 5. Image quantification How do we delineate brain anatomy and quantify phenotypes?
How to segment pathologies such as white-matter hyper-intensities?
02:30 6. Image quality control How do we identify image preprocessing failures?
03:00 7. Statistical analysis (Part 1: ROIs) How to look at group differences in regional anatomical features?
03:30 8. Statistical analysis (Part 2: voxels) How to look at group differences at voxel-level features?
04:00 9. Reproducibility considerations How sensitive are the findings to your MR pipeline parameters?
04:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.