Index

A

add_javascript_function() (in module pybraincompare.template.templates) add_string() (in module pybraincompare.template.templates) addNodes() (pybraincompare.annotate.JSONEncoder.NodeDict method)

animate_figure() (in module pybraincompare.report.animate) apply_threshold() (in module pybraincompare.compare.mrutils) atlas (class in pybraincompare.compare.atlas)

C

calc_rows_columns() (in module pybraincompare.compare.maths) calculate_atlas_correlation() (in module pybraincompare.compare.maths) calculate_correlation() (in module pybraincompare.compare.maths) calculate_pairwise_correlation() (in module pybraincompare.compare.maths) calculate_similarity_search() (in module pybraincompare.compare.search)

central_tendency() (in module pybraincompare.report.qa) connectogram() (in module pybraincompare.compare.network) count_voxels() (in module pybraincompare.report.qa) create_glassbrain_portfolio() (in module pybraincompare.compare.search)

D

default() (pybraincompare.annotate.JSONEncoder.NodeJSONEncoder method) do_mask() (in module pybraincompare.compare.mrutils)

do_multi_correlation() (in module pybraincompare.compare.maths)

G

generate_thresholds() (in module pybraincompare.compare.mrutils) get_atlas_objects() (in module pybraincompare.compare.scatterplot) get_colors() (in module pybraincompare.report.colors) get_data_directory() (in module pybraincompare.mr.datasets) get_histogram_data() (in module pybraincompare.report.histogram) get_image() (in module pybraincompare.template.templates) get_mni_atlas() (in module pybraincompare.mr.datasets) get_name() (in module pybraincompare.template.futils) get_nii_obj() (in module pybraincompare.compare.mrutils) get_package_dir() (in module pybraincompare.template.futils)

get_pair_images() (in module pybraincompare.mr.datasets) get_percent_nonzero() (in module pybraincompare.report.qa) get_region_names() (pybraincompare.compare.atlas.atlas method) get_standard_brain() (in module pybraincompare.compare.mrutils) (in module pybraincompare.mr.datasets) get_standard_mask() (in module pybraincompare.compare.mrutils) (in module pybraincompare.mr.datasets) get_standard_mat() (in module pybraincompare.compare.mrutils) get_static_svg() (pybraincompare.compare.atlas.atlas method) get_svg_html() (in module pybraincompare.template.visual) get_template() (in module pybraincompare.template.templates) get_voxel_range() (in module pybraincompare.report.qa)

H

header_metrics() (in module pybraincompare.report.qa)

histogram_image() (in module pybraincompare.report.histogram)

I

internal_view() (in module pybraincompare.template.visual) is_only_positive() (in module pybraincompare.report.qa)

is_thresholded() (in module pybraincompare.report.qa)

M

make_anat_image() (in module pybraincompare.report.image) make_binary_deletion_mask() (in module pybraincompare.compare.mrutils) make_binary_deletion_vector() (in module pybraincompare.compare.mrutils) make_color_lookup() (pybraincompare.compare.atlas.atlas method) make_dir() (in module pybraincompare.template.futils) make_glassbrain_image() (in module pybraincompare.report.image) make_in_out_mask() (in module pybraincompare.compare.mrutils) make_ontology_tree_d3() (in module pybraincompare.annotate.ontology) make_png_paths() (in module pybraincompare.template.futils)

make_resampled_transformation() (in module pybraincompare.mr.transformation) make_resampled_transformation_vector() (in module pybraincompare.mr.transformation) make_reverse_inference_tree_d3() (in module pybraincompare.annotate.ontology) make_roi_image() (in module pybraincompare.report.image) make_scatterplot_interface() (in module pybraincompare.compare.scatterplot) make_stat_image() (in module pybraincompare.report.image) make_svg() (pybraincompare.compare.atlas.atlas method) make_tmp_folder() (in module pybraincompare.template.futils)

N

named_ontology_tree_from_tsv() (in module pybraincompare.annotate.ontology) Node (class in pybraincompare.annotate.JSONEncoder)

NodeDict (class in pybraincompare.annotate.JSONEncoder) NodeJSONEncoder (class in pybraincompare.annotate.JSONEncoder)

O

ontology_tree_from_tsv() (in module pybraincompare.annotate.ontology)

outliers() (in module pybraincompare.report.qa)

P

percent_to_float() (in module pybraincompare.compare.maths) peterson_roi_labels() (in module pybraincompare.report.colors) plot_histogram() (in module pybraincompare.report.histogram) plot_vline() (in module pybraincompare.report.image) pybraincompare (module) pybraincompare.annotate (module) pybraincompare.annotate.JSONEncoder (module) pybraincompare.annotate.ontology (module) pybraincompare.compare (module) pybraincompare.compare.atlas (module) pybraincompare.compare.maths (module) pybraincompare.compare.mrutils (module) pybraincompare.compare.network (module) pybraincompare.compare.scatterplot (module) pybraincompare.compare.search (module) pybraincompare.mr (module) pybraincompare.mr.datasets (module) pybraincompare.mr.transformation (module)

pybraincompare.report (module) pybraincompare.report.animate (module) pybraincompare.report.colors (module) pybraincompare.report.histogram (module) pybraincompare.report.image (module) pybraincompare.report.qa (module) pybraincompare.report.webreport (module) pybraincompare.template (module) pybraincompare.template.futils (module) pybraincompare.template.templates (module) pybraincompare.template.visual (module) pybraincompare.testing (module) pybraincompare.testing.test_correlation (module) pybraincompare.testing.test_histogram (module) pybraincompare.testing.test_masking (module) pybraincompare.testing.test_scatterplot_compare (module) pybraincompare.testing.test_transformation (module)

R

random_colors() (in module pybraincompare.report.colors) read_template() (in module pybraincompare.template.templates) read_xml() (pybraincompare.compare.atlas.atlas method) region (class in pybraincompare.compare.atlas) remove_attributes() (pybraincompare.compare.atlas.atlas method)

remove_resources() (in module pybraincompare.template.templates) resample_images_ref() (in module pybraincompare.compare.mrutils) run_qa() (in module pybraincompare.report.webreport) run_webserver() (in module pybraincompare.template.visual)

S

save_svg() (pybraincompare.compare.atlas.atlas method) save_template() (in module pybraincompare.template.templates) scatterplot_canvas() (in module pybraincompare.compare.scatterplot) scatterplot_compare() (in module pybraincompare.compare.scatterplot) scatterplot_compare_error() (in module pybraincompare.compare.scatterplot)

scatterplot_compare_vector() (in module pybraincompare.compare.scatterplot) set_attributes() (pybraincompare.compare.atlas.atlas method) similarity_search() (in module pybraincompare.compare.search) squeeze_fourth_dimension() (in module pybraincompare.compare.mrutils)

T

t_to_z() (in module pybraincompare.report.qa) test_binary_deletion_mask() (in module pybraincompare.testing.test_masking) test_binary_deletion_mask_values() (in module pybraincompare.testing.test_masking) test_binary_deletion_vector() (in module pybraincompare.testing.test_masking) test_histogram_output() (in module pybraincompare.testing.test_histogram)

test_masked_transformation() (in module pybraincompare.testing.test_transformation) test_scatterplot_error_message() (in module pybraincompare.testing.test_scatterplot_compare) test_simulated_correlations() (in module pybraincompare.testing.test_correlation) test_unmasked_transformation() (in module pybraincompare.testing.test_transformation)

U

unwrap_list_unique() (in module pybraincompare.template.futils)

unzip() (in module pybraincompare.template.futils)

V

view() (in module pybraincompare.template.visual)