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Practice and theory of brain imaging

The neuroimaging problem

The problem and the plan

The tools

Ode to code
Surviving the computer
Our tools
Using Jupyter notebooks
More on the Jupyter notebook
Brisk introduction to Python
Installing on your computer

Images and code and images

Using the pathlib module
What is an image?
Introduction to Numpy
Boolean arrays
Two-dimensions, reshaping
Arrays as images, images as arrays
Three-dimensional arrays
Three-dimensional images, NIfTI
Reshaping and three-dimensional arrays
Indexing with Boolean arrays
Boolean indexing with more than one dimension
Working with four dimensional images, masks and functions
Reshaping, 4D to 2D
Voxels and time

Working reproducibly

Modules and scripts
Where does Python look for modules?
Using assert for testing
Python coding style
Docstrings
Module directories
On testing

Detecting activation

Correlating with voxel time courses
Convolution
Convolving with the hemodyamic response function
Introducing regression
Regression for a single voxel
Notation for regression models
Introduction to the general linear model
A worked example of the general linear model
Modeling a single voxel
Estimation for many voxels at the same time
Hypothesis testing with the general linear model
Testing a single voxel
Using onsets that do not start on a TR
Whole-brain t tests and p values
Notes on the Bonferroni threshold

Spatial processing

Slice timing correction
Calculating transformations between images
Encoding zooms (scaling) with a diagonal matrix
The nibabel.affines module
Applying coordinate transforms with nibabel.affines.apply_affine
General resampling between images with scipy.ndimage.map_coordinates
The image header and affine
Images and affines
Rotations and rotation matrices
Resampling with scipy.ndimage
Registration with dipy
Anterior cingulate

Notes on arrays and plots

Methods vs functions in NumPy
Testing for near equality with “allclose”
NumPy arange
Logical operations on Boolean arrays
Vector and matrix dot products, “np.outer”
Adding length 1 dimensions with newaxis
Array reduction operations
Numpy random number generators
Subtracting the mean from columns or rows
Plotting lines in matplotlib
Subplots and axes in matplotlib

Repository
Open issue

Index

By The nipraxis team

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