├── .coveragerc ├── .gitattributes ├── .gitignore ├── .mailmap ├── .travis.yml ├── AUTHOR ├── LICENSE ├── MANIFEST.in ├── README.rst ├── THANKS ├── doc ├── .gitignore ├── Makefile ├── README.txt ├── _static │ ├── nipy.css │ └── reggie2.png ├── _templates │ └── layout.html ├── api │ └── index.rst ├── bibtex │ ├── README.txt │ └── vtk.bib ├── conf.py ├── devel │ ├── code_discussions │ │ ├── brainvisa_repositories.rst │ │ ├── comparisons │ │ │ ├── index.rst │ │ │ └── vtk_datasets.rst │ │ ├── coordmap_notes.rst │ │ ├── image_ordering.rst │ │ ├── index.rst │ │ ├── pipelining_api.rst │ │ ├── refactoring │ │ │ ├── imagelists.rst │ │ │ └── index.rst │ │ ├── registration_api.rst │ │ ├── repository_api.rst │ │ ├── repository_design.rst │ │ ├── simple_viewer.rst │ │ ├── understanding_affines.rst │ │ └── usecases │ │ │ ├── batching.rst │ │ │ ├── images.rst │ │ │ ├── index.rst │ │ │ ├── resampling.rst │ │ │ └── transformations.rst │ ├── development_quickstart.rst │ ├── doctests_preprocessor.rst │ ├── guidelines │ │ ├── changelog.rst │ │ ├── commit_codes.rst │ │ ├── compiling_windows.rst │ │ ├── coverage_testing.rst │ │ ├── debugging.rst │ │ ├── elegant.py │ │ ├── gitwash │ │ │ ├── branch_list.png │ │ │ ├── branch_list_compare.png │ │ │ ├── configure_git.rst │ │ │ ├── development_workflow.rst │ │ │ ├── dot2_dot3.rst │ │ │ ├── following_latest.rst │ │ │ ├── forking_button.png │ │ │ ├── forking_hell.rst │ │ │ ├── git_development.rst │ │ │ ├── git_install.rst │ │ │ ├── git_intro.rst │ │ │ ├── git_links.inc │ │ │ ├── git_resources.rst │ │ │ ├── index.rst │ │ │ ├── patching.rst │ │ │ ├── pull_button.png │ │ │ └── set_up_fork.rst │ │ ├── howto_document.rst │ │ ├── index.rst │ │ ├── make_release.rst │ │ ├── open_source_devel.rst │ │ ├── optimization.rst │ │ ├── sphinx_helpers.rst │ │ └── testing.rst │ ├── images.rst │ ├── index.rst │ ├── install │ │ ├── debian.rst │ │ ├── fedora.rst │ │ ├── index.rst │ │ ├── windows.rst │ │ └── windows_scipy_build.rst │ ├── planning │ │ ├── TODO.rst │ │ ├── index.rst │ │ └── roadmap.rst │ └── tools │ │ ├── index.rst │ │ ├── tricked_out_emacs.rst │ │ └── virtualenv-tutor.rst ├── documentation.rst ├── faq │ ├── documentation_faq.rst │ ├── index.rst │ ├── johns_bsd_pitch.rst │ ├── licensing.rst │ └── why.rst ├── glossary.rst ├── history.rst ├── index.rst ├── labs │ ├── datasets.rst │ ├── datasets │ │ ├── viz_volume_data.py │ │ ├── viz_volume_field.py │ │ ├── viz_volume_grid.py │ │ ├── viz_volume_img.py │ │ ├── volume_data.jpg │ │ ├── volume_field.jpg │ │ ├── volume_grid.jpg │ │ └── volume_img.jpg │ ├── enn.rst │ ├── index.rst │ ├── mask.rst │ ├── plots │ │ ├── enn_demo.py │ │ └── surrogate_array.py │ ├── simul_activation.rst │ ├── viz.png │ └── viz.rst ├── license.rst ├── links_names.txt ├── mission.rst ├── mission.txt ├── publications.rst ├── references │ └── brainpy_abstract.rst ├── sphinxext │ ├── README.txt │ ├── autosummary_generate.py │ ├── ipython_console_highlighting.py │ └── numpy_ext │ │ ├── __init__.py │ │ ├── docscrape.py │ │ ├── docscrape_sphinx.py │ │ └── numpydoc.py └── users │ ├── basic_io.rst │ ├── coordinate_map.rst │ ├── glm_spec.rst │ ├── index.rst │ ├── install_data.rst │ ├── installation.rst │ ├── introduction.rst │ ├── math_coordmap.rst │ ├── plots │ ├── amplitudes.py │ ├── block.py │ ├── event.py │ ├── event_amplitude.py │ ├── hrf.py │ ├── hrf_delta.py │ ├── hrf_different.py │ ├── neuronal_block.py │ ├── neuronal_event.py │ ├── random_amplitudes.py │ ├── random_amplitudes_times.py │ └── sinusoidal.py │ ├── scipy_orientation.rst │ └── tutorial.rst ├── examples ├── affine_registration.py └── space_time_realign.py ├── nireg ├── NOTES_ELF ├── TODO.txt ├── __init__.py ├── _register.c ├── _register.h ├── _register.pyx ├── affine.py ├── chain_transform.py ├── cubic_spline.c ├── cubic_spline.h ├── externals │ ├── __init__.py │ ├── argparse.py │ ├── configobj.py │ ├── setup.py │ ├── six.py │ ├── transforms3d │ │ ├── __init__.py │ │ ├── quaternions.py │ │ ├── setup.py │ │ ├── taitbryan.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── samples.py │ │ │ ├── test_quaternions.py │ │ │ └── test_taitbryan.py │ │ └── utils.py │ └── validate.py ├── groupwise_registration.py ├── histogram_registration.py ├── joint_histogram.c ├── joint_histogram.h ├── np_distutils_monkey.py ├── optimizer.py ├── polyaffine.c ├── polyaffine.h ├── polyaffine.py ├── resample.py ├── setup.py ├── similarity_measures.py ├── slicetiming │ ├── __init__.py │ ├── setup.py │ ├── tests │ │ ├── __init__.py │ │ └── test_timefuncs.py │ └── timefuncs.py ├── testing │ ├── __init__.py │ ├── anatomical.nii.gz │ ├── functional.nii.gz │ └── setup.py ├── tests │ ├── __init__.py │ ├── test_affine.py │ ├── test_chain_transforms.py │ ├── test_cubic_spline.py │ ├── test_fmri_realign4d.py │ ├── test_histogram_registration.py │ ├── test_polyaffine.py │ ├── test_register.py │ ├── test_resample.py │ ├── test_slice_timing.py │ └── test_transform.py ├── transform.py ├── type_check.py ├── wichmann_prng.c └── wichmann_prng.h ├── 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