Course Introduction

Medical Imaging Modalities

Figure 1

X-ray image creation schematic.
Schematic of x-ray image creation.

Figure 2

Mitral valve prolapse.
Image of mitral valve prolapse from Cafer Zorkun, MD, PhD on wikidoc.org with creative commons lisence.

Working with MRI

Figure 1

FLAIR brain

Figure 2

FMRI

Figure 3

FMRI timeseries

Figure 4

DWIDWI tracts

Figure 5

Numpy arrays

Figure 6

MRI slices

Figure 7

T1 weighted

Figure 8

Coordinate system

Figure 9

4D array time

Figure 10

Nipreps chart

Figure 11

dMRI preprocess steps

Registration and Segmentation with SITK

Figure 1

SITK logo.

Figure 2

SITK Image.
An image in SITK occupies a region in physical space which is defined by its meta-data (origin, size, spacing, and direction cosine matrix). Note that the image’s physical extent starts half a voxel before the origin and ends half a voxel beyond the last voxel.

Figure 3

Isotropic vs non-isotropic images.
The same image displayed with a viewer that is not aware of spatial meta-data (left image) and one that is aware (right image). The image’s pixel spacing is (0.97656, 2.0)mm.

Figure 4

Spatial relationship in images.
Two images with exactly the same pixel data, positioned in the world coordinate system. In SITK these are not considered the same image, because they occupy different spatial locations.

Figure 5

Slice and cmaps example.

Figure 6

Multiple slices example.

Figure 7

Operations examples.

Figure 8

Slice with grid mask.

Figure 9

Digital x-ray image.

Figure 10

Grayscale x-ray image.

Figure 11

Non-isotropic slices example.

Figure 12

CT and MRI volumes before being aligned.

Figure 13

CT and MRI volumes overimposed.

Figure 14

Metrics across iterations.

Figure 15

CT and MRI volumes aligned.

Figure 16

T1 MRI scan, Z slices.

Figure 17

Basic thresholding methods.

Figure 18

Brain lateral ventricle.

Figure 19

Initial seed.

Figure 20

Region growing segmentations.

Figure 21

Confidence connected after morphological closing.

Figure 22

Level-set segmentation.

Figure 23

Y-axis segmentation.

Preparing Images for Machine Learning

Figure 1

CXR examples

Figure 2

augmented chest x-ray different sizes

Figure 3

augmented chest x-ray

Figure 4

augmented by shear chest x-ray

Figure 5

augmented by waves chest x-ray

Figure 6

T1 v T3

Anonymizing Medical Images

Figure 1

Defacing examples
Image from “A reproducibility evaluation of the effects of MRI defacing on brain segmentation” by Chenyu Gao, Bennett A. Landman, Jerry L. Prince, and Aaron Carass. The preprint is available here.

Figure 2

jewlery artifact
Case courtesy of Ian Bickle, Radiopaedia.org. From the case rID: 61830

Generative AI in Medical Imaging

Figure 1

Misled image
Image generated by Dr. Candace Makeda Moore prompting Adobe Firely.

Figure 2

Misled image of cats
Image generated by Dr. Candace Makeda Moore prompting Adobe Firely.