_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: intro
parts:
- caption: The neuroimaging problem
  chapters:
  - file: the_problem

- caption: The tools
  chapters:
  - file: to_code
  - file: surviving_computers
  - file: the_software
  - file: using_jupyter
  - file: more_on_jupyter
  - file: brisk_python
  - file: installation

- caption: Images and code and images
  chapters:
  - file: pathlib
  - file: what_is_an_image
  - file: numpy_intro
  # arrays exercise
  - file: boolean_arrays
  - file: reshape_and_2d
  - file: arrays_and_images
  # camera exercise
  - file: arrays_3d
  - file: images_3d
  - file: reshape_and_3d
  # anatomical exercise
  - file: boolean_indexing
  - file: boolean_indexing_nd
  - file: intro_to_4d
  - file: reshape_and_4d
  - file: voxels_by_time

- caption: Working reproducibly
  chapters:
  - file: on_modules
  - file: sys_path
  - file: assert
  - file: coding_style
  - file: docstrings
  - file: module_directories
  - file: on_testing

- caption: Detecting activation
  chapters:
  - file: voxel_time_courses
  - file: on_convolution
  - file: convolution_background
  - file: on_regression
  - file: regress_one_voxel
  - file: regression_notation
  - file: glm_intro
  - file: mean_test_example
  - file: model_one_voxel
  - file: multi_multiply
  - file: hypothesis_tests
  - file: test_one_voxel
  - file: non_tr_onsets
  - file: whole_image_statistics
  - file: bonferroni_correction

- caption: Spatial processing
  chapters:
  - file: slice_timing
  - file: optimizing_space
  - file: diagonal_zooms
  - file: nibabel_affines
  - file: nibabel_apply_affine
  - file: map_coordinates
  - file: image_header_and_affine
  - file: images_and_affines
  - file: rotation_2d_3d
  - file: resampling_with_ndimage
  - file: dipy_registration
  - file: anterior_cingulate

- caption: Notes on arrays and plots
  chapters:
  - file: methods_vs_functions
  - file: allclose
  - file: arange
  - file: numpy_logical
  - file: dot_outer
  - file: newaxis
  - file: array_reductions
  - file: numpy_random
  - file: subtract_means
  - file: plot_lines
  - file: subplots