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日期:2021-05-15 11:09

CS463/516 assignment 1

Due: Thursday, May 27th at 11:59 PM (Eastern time).

Submit: a pdf report showing your source code, displayed images, and any explanation/notes.

Topic: Basic numpy, medical imaging modalities, SNR, and denoising

In this assignment we will familiarize ourselves with basic numpy array manipulation, different imaging

modalities, and gain understanding of some basic image features (contrast and SNR).

Setup

First, install spyder (or any python IDE). If you are on windows, you will probably want to install

anaconda first: https://docs.anaconda.com/anaconda/install/

? Note – you don’t need to use spyder (any python IDE is fine) but it will help a lot in this course

because the ipython console is very useful for debugging and visualization of intermediate

results.

Second, get the images (link below). This directory contains 8 images:

The images were all acquired using MRI scanner, with the exception of ct.nii.gz and meanpet.nii.gz,

which are from CT and PET scanner, respectively. Most of the images are 3D, with the exception of

cardiac_axial.nii.gz, cardiac_realtime.nii.gz, and fmri.nii.gz, which are 4D.

https://drive.google.com/file/d/10_bOHQmfe9WkTlK9Td5IhjVHhBp-s2ni/view?usp=sharing

Part 1: (25%): simple plotting with matplotlib

a) Display all images middle z-slice (3rd dimension, axis=2) (as seen below). Use the ‘jet’ color scale

(instead of the gray color scale that I use below in my example). Above each image, show the title of the

modality. Remove the x/y axis labels (as I did below). Use plt.subplot

b) display the minimum intensity projection (MIP) for the swi.nii.gz, and the maximum intensity

projection (MIP) for the TOF (in jet color map).

Left: part (a) – replicate this

but use jet color map

instead of gray.

Left: part (b). note how

the blood vessels are

displayed prominently

due to the projection.

You will need to restrict

the z-slices from the SWI

to achieve a good MIP.

Use np.min and

np.max.

Part 2 (25%): contrast estimation

Using numpy, get 3 different contrast measures for each image (root mean square, Michelson, and

entropy, see lecture 3 slide 4, 5). Report the contrast (all 3 versions) in the title of the plots in figure 1a.

base your contrast estimation on the entire 3D or 4D image (not just the slice shown in the figures).

Part 3 (25%): SNR estimation, quantifying noise

Using the method outlined in the lecture 3 slide 7, report the SNR for each of the modalities. Which

modality has the highest SNR and which has the lowest?

Plot histograms of the noise in each image. What type of distribution does the noise follow?

To display the solution to part 3, create a new figure (as in part 1) and display the noise histogram of

each image (instead of the image itself) in each sub plot. Show the SNR as the title above each histogram

(along with the image name).

*caution – when selecting your noise patch, be sure the patch isn’t all zeros, otherwise your noise will

be estimated as 0 and the SNR will be infinite*

Part 4 (25%): linear filtering

Using the Fourier transform method shown towards the end of lecture 2 video, apply linear filtering to

each image for ?? = 2, ?? = 4, and ?? = 15. Create 3 new versions of the figure in part 1a, one figure for

each sigma. Show the middle slice of the filtered image in all subplots.

Submission: Put all your figures in your pdf, along with the code used to generate them and any

comments you have about the work.

Bonus +5%:

Make a python class that can display 3d and 4d images (scroll through the slices and time points), similar

to AFNI’s method for time series display (see lecture 1 at time 58:12).


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