.. Practical Neuroimaging documentation master file, created by
   sphinx-quickstart on Thu Feb 14 15:37:53 2013.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

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Psych 214 |--| functional MRI methods
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*******************
Fall semester 2016.
*******************

This is a hands-on course teaching the principles of functional MRI (fMRI)
data analysis. We will teach you how to work with data and code to get a
deeper understanding of how fMRI methods work, how they can fail, how to fix
them, and how to develop new methods. We will cover the basic concepts in
neuroimaging analysis, and how they relate to the wider world of statistics,
engineering and computer science. At the same time we will teach you
techniques of data analysis that will make your work easier to organize,
understand, explain and share. At the end of the course we expect you to be
able to analyze fMRI data using Python and keep track of your work with
version control using git.

.. toctree::
    :maxdepth: 1

    syllabus
    preparation
    logistics
    classes_and_labs
    projects
    topics
    exercises
    example_data
    bibliography

.. The hidden toctree below is to suppress build warnings

.. toctree::
    :hidden:

    choosing_editor
    installation_on_mac
    installation_on_linux
    installation_on_windows
    brisk_python
    glossary
    mentors
    papers/index
    anatomical_exercise
    anatomical_solution
    arrays_and_images
    arteries_exercise
    arteries_solution
    camera_exercise
    camera_solution
    classwork/README
    classwork/day_00/introducing_python
    classwork/day_00/what_is_an_image
    lab_00
    lab_01_exercise
    lab_01_solution
    lab_02
    lab_03
    lab_04
    lab_05
    lab_06
    lab_07
    on_loops
    index_reshape
    reshape_and_3d
    four_dimensions_exercise
    four_dimensions_solution
    intro_to_4d
    on_modules
    dot_and_outer
    pca_exercise
    pca_solution
    path_manipulation
    allclose
    arange
    boolean_indexing
    correlation_2d_exercise
    correlation_2d_solution
    first_activation_exercise
    first_activation_solution
    list_comprehensions
    methods_vs_functions
    model_one_voxel
    newaxis
    packages_namespaces
    pearson_functions
    reshape_and_4d
    slicing_with_booleans
    sys_path
    two_dunders
    using_pythonpath
    voxel_correlation_exercise
    voxel_correlation_solution
    voxel_time_courses
    voxels_by_time
    dot_outer
    git_videos
    git_walk_through
    git_workflow_exercises
    github_pca_homework
    github_glm_homework
    numpy_logical
    plot_lines
    subplots
    subtract_means
    array_reductions
    diagnostics_project
    on_estimation_exercise
    on_estimation_solution
    mean_test_example
    on_dummies_exercise
    on_dummies_solution
    convolution_background
    floating_in_text
    diag_inverse
    subtract_mean_math
    hypothesis_tests
    github_dummies_homework
    make_an_hrf_exercise
    make_an_hrf_solution
    hrf_correlation_exercise
    hrf_correlation_solution
    non_tr_onsets
    multi_model_homework
    test_one_voxel
    multi_multiply
    multi_model_exercise
    multi_model_solution
    validate_against_scipy
    nans
    whole_image_statistics
    lab_09
    otsu_threshold
    slice_timing_exercise
    slice_timing_solution
    lab_10
    printing_floating
    image_header_and_affine
    more_on_rotation_exercise
    more_on_rotation_solution
    images_and_affines
    optimizing_rotation_exercise
    optimizing_rotation_solution
    resampling_with_ndimage
    reslicing_with_affines_exercise
    reslicing_with_affines_solution
    rotation_2d_3d.rst
    what_extra_transform_exercise
    what_extra_transform_solution
    project_grading
    coding_style
    string_literals
    docstrings
    keyword_arguments
    numpy_diag
    assert
    numpy_random
    nibabel_affines
    numpy_transpose
    numpy_squeeze
    optimizing_affine_exercise
    optimizing_affine_solution
    nibabel_apply_affine
    diagonal_zooms
    lab_11
    numpy_meshgrid
    map_coordinates
    applying_deformations_solution
    applying_deformations_exercise
    comparing_arrays
    comparing_floats
    saving_images
    string_formatting
    tr_and_headers
    truthiness
    dipy_registration
    anterior_cingulate
    participate
    introducing_nipype
    smoothing_solution
    smoothing_exercise
    spm_slice_timing_exercise
    spm_slice_timing_solution
    full_scripting
    lab_12
    classes
    labs
    participate_grading