Index

A

affine_initializer_wrapper() (in module unravel.register.affine_initializer) aggregate_files_from_sample_dirs() (in module unravel.utilities.aggregate_files_from_sample_dirs)

apply_rgb_to_cell() (in module unravel.cluster_stats.legend) AttrDict (class in unravel.core.config) AverageTimePerIterationColumn (class in unravel.core.utils)

C

calculate_fragments() (in module unravel.voxel_stats.vstats) calculate_regional_volumes() (in module unravel.cluster_stats.sunburst) calculate_top_regions() (in module unravel.cluster_stats.table) can_collapse() (in module unravel.cluster_stats.table) check_fdr_command() (in module unravel.voxel_stats.vstats) clean_tifs_dir() (in module unravel.utilities.clean_tif_dirs) cluster_index() (in module unravel.cluster_stats.fdr) cluster_summary() (in module unravel.cluster_stats.stats_table) cluster_validation_data_df() (in module unravel.cluster_stats.cstats) collapse_hierarchy() (in module unravel.cluster_stats.table) condition_selector() (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative)

Config (class in unravel.core.config) Configuration (class in unravel.core.config) convert_dtype() (in module unravel.image_io.io_nii) copy_files() (in module unravel.core.utils) copy_stats_files() (in module unravel.cluster_stats.org_data) cp() (in module unravel.cluster_stats.org_data) create_design_ttest2() (in module unravel.voxel_stats.vstats) CustomHelpAction (class in unravel.core.help_formatter) CustomMofNCompleteColumn (class in unravel.core.utils) CustomTimeElapsedColumn (class in unravel.core.utils) CustomTimeRemainingColumn (class in unravel.core.utils)

D

define_zarr_to_nii_output() (in module unravel.image_io.zarr_to_nii)

E

extract_unique_regions_from_file() (in module unravel.cluster_stats.legend)

F

fdr() (in module unravel.cluster_stats.fdr) fdr_range() (in module unravel.cluster_stats.fdr_range) fill_na_with_last_known() (in module unravel.cluster_stats.table) filter_dataframe() (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) filter_help_output() (unravel.core.help_formatter.RichArgumentParser method) filter_region_ids() (in module unravel.region_stats.rstats_mean_IF_summary)

filter_region_summary() (in module unravel.utilities.region_info) find_and_copy_files() (in module unravel.utilities.aggregate_files_recursively) find_incongruent_clusters() (in module unravel.cluster_stats.find_incongruent_clusters) find_largest_h5_file() (in module unravel.image_io.h5_to_tifs) find_matching_directory() (in module unravel.cluster_stats.org_data) find_max_intensity() (in module unravel.image_tools.max) format_argparse_help() (in module unravel.core.help_formatter) format_docstring_for_terminal() (in module unravel.core.help_formatter) format_usage() (unravel.core.help_formatter.RichArgumentParser method)

G

generate_summary_table() (in module unravel.cluster_stats.prism) generate_sunburst() (in module unravel.cluster_stats.index) generate_wireframe() (in module unravel.image_tools.atlas.wireframe) get_all_region_ids() (in module unravel.region_stats.rstats_mean_IF_summary) get_dir_name_from_args() (in module unravel.core.utils) get_fill_color() (in module unravel.cluster_stats.table) get_groups_info() (in module unravel.voxel_stats.vstats)

get_max_region_id_from_csvs() (in module unravel.region_stats.rstats_mean_IF_summary) get_pad_percent() (in module unravel.core.utils) get_region_details() (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) get_samples() (in module unravel.core.utils) get_top_regions_and_percent_vols() (in module unravel.cluster_stats.table) group_hemisphere_data() (in module unravel.cluster_stats.group_bilateral_data)

H

hedges_g() (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute)

I

initialize_progress_bar() (in module unravel.core.utils)

L

load_config() (in module unravel.core.utils) load_data() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary)

load_h5() (in module unravel.image_io.h5_to_tifs) load_text_from_file() (in module unravel.core.utils) log_command() (in module unravel.core.utils)

M

main() (in module unravel.cluster_stats.brain_model) (in module unravel.cluster_stats.clusters) (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) (in module unravel.cluster_stats.fdr) (in module unravel.cluster_stats.fdr_range) (in module unravel.cluster_stats.find_incongruent_clusters) (in module unravel.cluster_stats.group_bilateral_data) (in module unravel.cluster_stats.index) (in module unravel.cluster_stats.legend) (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.cluster_stats.org_data) (in module unravel.cluster_stats.prism) (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) (in module unravel.cluster_stats.stats_table) (in module unravel.cluster_stats.summary) (in module unravel.cluster_stats.sunburst) (in module unravel.cluster_stats.table) (in module unravel.image_io.h5_to_tifs) (in module unravel.image_io.io_nii) (in module unravel.image_io.nii_hd) (in module unravel.image_io.nii_to_tifs) (in module unravel.image_io.nii_to_zarr) (in module unravel.image_io.reorient_nii) (in module unravel.image_io.zarr_to_nii) (in module unravel.image_tools.atlas.relabel_nii) (in module unravel.image_tools.atlas.wireframe) (in module unravel.image_tools.avg) (in module unravel.image_tools.max) (in module unravel.image_tools.modify_labels) (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) (in module unravel.register.affine_initializer) (in module unravel.register.reg_check) (in module unravel.register.reg_check_brain_mask) (in module unravel.unravel_commands) (in module unravel.utilities.aggregate_files_from_sample_dirs) (in module unravel.utilities.aggregate_files_recursively) (in module unravel.utilities.clean_tif_dirs) (in module unravel.utilities.get_samples) (in module unravel.utilities.points_compressor) (in module unravel.utilities.prepend_conditions) (in module unravel.utilities.region_info) (in module unravel.utilities.rename) (in module unravel.utilities.toggle_samples) (in module unravel.voxel_stats.mirror) (in module unravel.voxel_stats.vstats) (in module unravel.warp.warp) mean_std_count() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) metadata_from_h5() (in module unravel.image_io.h5_to_tifs) mirror() (in module unravel.voxel_stats.mirror)

module unravel.cluster_stats.brain_model unravel.cluster_stats.clusters unravel.cluster_stats.cstats unravel.cluster_stats.effect_sizes.effect_sizes unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative unravel.cluster_stats.fdr unravel.cluster_stats.fdr_range unravel.cluster_stats.find_incongruent_clusters unravel.cluster_stats.group_bilateral_data unravel.cluster_stats.index unravel.cluster_stats.legend unravel.cluster_stats.mean_IF_summary unravel.cluster_stats.org_data unravel.cluster_stats.prism unravel.cluster_stats.recursively_mirror_rev_cluster_indices unravel.cluster_stats.stats_table unravel.cluster_stats.summary unravel.cluster_stats.sunburst unravel.cluster_stats.table unravel.core.config unravel.core.help_formatter unravel.core.utils unravel.image_io.h5_to_tifs unravel.image_io.io_nii unravel.image_io.nii_hd unravel.image_io.nii_to_tifs unravel.image_io.nii_to_zarr unravel.image_io.reorient_nii unravel.image_io.zarr_to_nii unravel.image_tools.atlas.relabel_nii unravel.image_tools.atlas.wireframe unravel.image_tools.avg unravel.image_tools.max unravel.image_tools.modify_labels unravel.region_stats.rstats_mean_IF_summary unravel.region_stats.rstats_summary unravel.register.affine_initializer unravel.register.reg_check unravel.register.reg_check_brain_mask unravel.unravel_commands unravel.utilities.aggregate_files_from_sample_dirs unravel.utilities.aggregate_files_recursively unravel.utilities.clean_tif_dirs unravel.utilities.get_samples unravel.utilities.points_compressor unravel.utilities.prepend_conditions unravel.utilities.region_info unravel.utilities.rename unravel.utilities.toggle_samples unravel.voxel_stats.mirror unravel.voxel_stats.vstats unravel.warp.warp

N

nii_to_ndarray() (in module unravel.image_io.nii_to_zarr)

nii_to_tifs() (in module unravel.image_io.nii_to_tifs)

O

organize_validation_data() (in module unravel.cluster_stats.org_data)

P

pack_points() (in module unravel.utilities.points_compressor) parse_args() (in module unravel.cluster_stats.brain_model) (in module unravel.cluster_stats.clusters) (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) (in module unravel.cluster_stats.fdr) (in module unravel.cluster_stats.fdr_range) (in module unravel.cluster_stats.find_incongruent_clusters) (in module unravel.cluster_stats.group_bilateral_data) (in module unravel.cluster_stats.index) (in module unravel.cluster_stats.legend) (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.cluster_stats.org_data) (in module unravel.cluster_stats.prism) (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) (in module unravel.cluster_stats.stats_table) (in module unravel.cluster_stats.summary) (in module unravel.cluster_stats.sunburst) (in module unravel.cluster_stats.table) (in module unravel.image_io.h5_to_tifs) (in module unravel.image_io.io_nii) (in module unravel.image_io.nii_hd) (in module unravel.image_io.nii_to_tifs) (in module unravel.image_io.nii_to_zarr) (in module unravel.image_io.reorient_nii) (in module unravel.image_io.zarr_to_nii) (in module unravel.image_tools.atlas.relabel_nii) (in module unravel.image_tools.atlas.wireframe) (in module unravel.image_tools.avg) (in module unravel.image_tools.max) (in module unravel.image_tools.modify_labels) (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) (in module unravel.register.affine_initializer) (in module unravel.register.reg_check) (in module unravel.register.reg_check_brain_mask) (in module unravel.unravel_commands) (in module unravel.utilities.aggregate_files_from_sample_dirs) (in module unravel.utilities.aggregate_files_recursively) (in module unravel.utilities.clean_tif_dirs) (in module unravel.utilities.get_samples) (in module unravel.utilities.points_compressor) (in module unravel.utilities.prepend_conditions) (in module unravel.utilities.region_info) (in module unravel.utilities.rename) (in module unravel.utilities.toggle_samples) (in module unravel.voxel_stats.mirror) (in module unravel.voxel_stats.vstats) (in module unravel.warp.warp)

parse_color_argument() (in module unravel.region_stats.rstats_summary) perform_t_tests() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary) perform_tukey_test() (in module unravel.cluster_stats.cstats) plot_data() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary) points_compressor() (in module unravel.utilities.points_compressor) prepend_conditions() (in module unravel.utilities.prepend_conditions) print_func_name_args_times() (in module unravel.core.utils) print_help() (unravel.core.help_formatter.RichArgumentParser method) process_and_plot_data() (in module unravel.region_stats.rstats_summary) process_fdr_and_clusters() (in module unravel.cluster_stats.fdr) process_file() (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) process_files_with_glob() (in module unravel.core.utils) process_intensity() (in module unravel.image_tools.atlas.wireframe)

R

relative_hedges_g() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) remove_zero_intensity_regions() (in module unravel.region_stats.rstats_mean_IF_summary) rename_files() (in module unravel.utilities.rename) rename_items() (in module unravel.utilities.prepend_conditions) render() (unravel.core.utils.AverageTimePerIterationColumn method) (unravel.core.utils.CustomMofNCompleteColumn method) (unravel.core.utils.CustomTimeElapsedColumn method) (unravel.core.utils.CustomTimeRemainingColumn method)

reorient_nii() (in module unravel.image_io.reorient_nii) retain_labels() (in module unravel.image_tools.modify_labels) reverse_clusters() (in module unravel.cluster_stats.fdr) RichArgumentParser (class in unravel.core.help_formatter) run_randomise_parallel() (in module unravel.voxel_stats.vstats) run_script() (in module unravel.cluster_stats.summary) run_with_timeout() (in module unravel.register.affine_initializer)

S

save_as_nii() (in module unravel.image_io.zarr_to_nii) save_as_tifs() (in module unravel.image_io.h5_to_tifs) save_as_zarr() (in module unravel.image_io.nii_to_zarr) set_labels() (in module unravel.image_tools.modify_labels) SM (class in unravel.core.help_formatter) smart_float_format() (in module unravel.cluster_stats.fdr_range)

sort_samples() (in module unravel.cluster_stats.prism) sort_sunburst_hierarchy() (in module unravel.cluster_stats.table) split_clusters_based_on_effect() (in module unravel.cluster_stats.fdr) summarize_points() (in module unravel.utilities.points_compressor) summarize_significance() (in module unravel.region_stats.rstats_summary) sunburst() (in module unravel.cluster_stats.sunburst) SuppressMetavar (class in unravel.core.help_formatter)

T

transform_nii_affine() (in module unravel.image_io.reorient_nii)

U

undo_fill_with_original() (in module unravel.cluster_stats.table) unpack_points() (in module unravel.utilities.points_compressor) unravel.cluster_stats.brain_model module unravel.cluster_stats.clusters module unravel.cluster_stats.cstats module unravel.cluster_stats.effect_sizes.effect_sizes module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module unravel.cluster_stats.fdr module unravel.cluster_stats.fdr_range module unravel.cluster_stats.find_incongruent_clusters module unravel.cluster_stats.group_bilateral_data module unravel.cluster_stats.index module unravel.cluster_stats.legend module unravel.cluster_stats.mean_IF_summary module unravel.cluster_stats.org_data module unravel.cluster_stats.prism module unravel.cluster_stats.recursively_mirror_rev_cluster_indices module unravel.cluster_stats.stats_table module unravel.cluster_stats.summary module unravel.cluster_stats.sunburst module unravel.cluster_stats.table module unravel.core.config module unravel.core.help_formatter module unravel.core.utils module unravel.image_io.h5_to_tifs module unravel.image_io.io_nii module unravel.image_io.nii_hd module

unravel.image_io.nii_to_tifs module unravel.image_io.nii_to_zarr module unravel.image_io.reorient_nii module unravel.image_io.zarr_to_nii module unravel.image_tools.atlas.relabel_nii module unravel.image_tools.atlas.wireframe module unravel.image_tools.avg module unravel.image_tools.max module unravel.image_tools.modify_labels module unravel.region_stats.rstats_mean_IF_summary module unravel.region_stats.rstats_summary module unravel.register.affine_initializer module unravel.register.reg_check module unravel.register.reg_check_brain_mask module unravel.unravel_commands module unravel.utilities.aggregate_files_from_sample_dirs module unravel.utilities.aggregate_files_recursively module unravel.utilities.clean_tif_dirs module unravel.utilities.get_samples module unravel.utilities.points_compressor module unravel.utilities.prepend_conditions module unravel.utilities.region_info module unravel.utilities.rename module unravel.utilities.toggle_samples module unravel.voxel_stats.mirror module unravel.voxel_stats.vstats module unravel.warp.warp module

V

valid_clusters_t_test() (in module unravel.cluster_stats.cstats) verbose (unravel.core.config.Configuration attribute)

verbose_end_msg() (in module unravel.core.utils) verbose_start_msg() (in module unravel.core.utils)

W

warp() (in module unravel.warp.warp)

Z

zarr_to_ndarray() (in module unravel.image_io.zarr_to_nii)