mri2fem-lectures

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mri2fem-lectures

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Lecture series on From magnetic resonance imaging to finite element simulation

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# About these lectures #

This is a series of guest lectures given as part of the University of
Bergen's Porous Media Short Course Series in the Spring of 2021 . The
lectures are given online via Zoom on Jan 15, 22 and 29 at 14-16 CET.

Update: Also includes the slides of a Guest Lecture given as part of 
MAE 207: Finite Element Analysis for Coupled Problems at the University
of California San Diego, Nov 8 2022.

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

## Lecture schedule ##

I will roughly follow the following schedule each week:

- 14:00-14:45: Lecture
- 14:45-14:55: Break
- 14:55-15:00: Questions
- 15:00-15:45: Lecture
- 15:45-15:55: More questions

Please post questions in the chat. I will address questions from the
chat after the break and at the end.

## Prior knowledge ##

These lectures assume that you, the reader or audience, have

* Some knowledge of partial differential equations (PDEs) and finite
  element methods (FEM)
* Some knowledge of programming (Python, bash)
* No to some knowledge of brain physiology and imaging
* Knowledge of/Interest in using command-line tools

[The FEniCS tutorial](https://fenicsproject.org/tutorial/) by
Langtangen and Logg (2017) is a very good introduction to all of the
above.

## YouTube resources  ##

Tutorial video snippets are posted on [my mri2fem YouTube channel](https://youtube.com/playlist?list=PL2H4xO8DvXwVNy7EelY_TuYUgvQ4Dw_Lz) and include:

1. Downloading the MRI2FEM data set, viewing and extracting MR series
   using DICOM Browser
2. Viewing the FreeSurfer output
3. Creating a mesh of the left hemisphere using SVM-Tk from FreeSurfer surfaces
4. Simulating diffusion over the left hemisphere using FEniCS
5. Creating a mesh of the left hemisphere conforming to gray and white matter
6. Extracting the ventricular system and removing it from the left hemisphere
7. Creating a full brain mesh conforming to the gray/white matter and ventricles

## Tips for lecturing via Zoom ##

These lectures are given via two devices: one laptop (screen) mainly
used for seeing the audience and the chat; an iPad and iPencil running
Goodnotes for showing slides with easy annotation, following links to
online material (Zenodo, Github) including videos from YouTube.

Do a practice run of each lecture in before-hand.

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