Welcome to brainload’s documentation!

Contents:

• Brainload API Documentation
  • annot()
  • detect_subjects_in_directory()
  • export_mesh_nocolor_to_file()
  • fsaverage_mesh()
  • group()
  • group_native()
  • hemi_range()
  • label()
  • mesh_to_obj()
  • mesh_to_ply()
  • read_subjects_file()
  • rhi()
  • rhv()
  • stat()
  • subject()
  • subject_avg()
  • subject_data_native()
  • subject_data_standard()
  • subject_mesh()
  • Submodules
  • brainload.freesurferdata module
    • fsaverage_mesh()
    • get_morphometry_file_path()
    • get_num_fsaverage_verts_per_hemi()
    • get_standard_space_morphometry_file_path()
    • get_surface_file_path()
    • get_vox2ras_and_ras2vox_from_nifti_file()
    • group()
    • group_native()
    • hemi_range()
    • load_subject_mesh_files()
    • load_subject_morphometry_data_files()
    • merge_morphometry_data()
    • parse_talairach_file()
    • read_fs_morphometry_data_file_and_record_meta_data()
    • read_fs_surface_file_and_record_meta_data()
    • read_lookup_file()
    • read_m3z_file()
    • read_mgh_file()
    • read_mgh_header_matrices()
    • rhi()
    • rhv()
    • subject()
    • subject_avg()
    • subject_data_native()
    • subject_data_standard()
    • subject_mesh()
  • brainload.annotations module
    • AnnotQuery
      • AnnotQuery.compute_labels()
      • AnnotQuery.get_vertex_label_colors()
      • AnnotQuery.get_vertex_label_names()
    • annot()
    • color_rgbt_to_rgba()
    • get_atlas_region_names()
    • get_atlas_region_names_hardcoded()
    • label()
    • label_to_mask()
    • mask_data_using_label()
    • read_annotation_md()
    • read_label_md()
    • read_vertex_list_file()
    • region_data_native()
    • region_stats()
    • vertices_to_label()
  • brainload.nitools module
    • detect_subjects_in_directory()
    • do_subject_files_exist()
    • fill_template_filename()
    • load_vertex_indices()
    • load_voxel_indices()
    • read_BIDS_participants_file()
    • read_subjects_file()
    • save_vertex_indices()
    • write_BIDS_participants_file()
    • write_lines_to_text_file()
    • write_subjects_file()
  • brainload.brainlocate module
    • BrainLocate
      • BrainLocate.get_closest_vertex()
      • BrainLocate.get_closest_vertex_and_distance()
  • brainload.brainvoxlocate module
    • BrainVoxLocate
      • BrainVoxLocate.get_closest_not_unknown()
      • BrainVoxLocate.get_ras_coords_at_voxel_crs()
      • BrainVoxLocate.get_voxel_crs_at_ras_coords()
      • BrainVoxLocate.get_voxel_segmentation_labels()
  • brainload.brainwrite module
    • get_surface_vertices_overlay_text_file_lines()
    • get_surface_vertices_overlay_volume_data()
    • get_surface_vertices_overlay_volume_data_1color()
    • get_volume_data_with_custom_marks()
    • write_voldata_to_mgh_file()
    • write_voldata_to_nifti_file()
  • brainload.stats module
    • extract_column_from_table_data()
    • extract_field_from_table_data()
    • extract_table_data_indices_where()
    • get_stats_table_column_names()
    • group_stats()
    • group_stats_aparc()
    • group_stats_aparc_DKTatlas()
    • group_stats_aparc_a2009s()
    • group_stats_aseg()
    • group_stats_by_row()
    • measures_to_numpy()
    • parse_curve_stats()
    • parse_curve_stats_file()
    • register_dat_matrix()
    • stat()
    • stats_table_region_label_column_name()
    • stats_table_to_numpy()
    • stats_table_to_numpy_by_row()
    • typelist_for_aparc_atlas_stats()
    • typelist_for_aseg_stats()
  • brainload.surfacegraph module
  • brainload.braindescriptors module
    • BrainDescriptors
      • BrainDescriptors.add_curv_stats()
      • BrainDescriptors.add_custom_measure_stats()
      • BrainDescriptors.add_parcellation_stats()
      • BrainDescriptors.add_segmentation_stats()
      • BrainDescriptors.add_single_segmentation_stats()
      • BrainDescriptors.add_standard_stats()
      • BrainDescriptors.check_for_NaNs()
      • BrainDescriptors.check_for_curv_stats_files()
      • BrainDescriptors.check_for_custom_measure_stats_files()
      • BrainDescriptors.check_for_hemi_dependent_file()
      • BrainDescriptors.check_for_hemi_independent_file()
      • BrainDescriptors.check_for_parcellation_stats_files()
      • BrainDescriptors.check_for_segmentation_stats_files()
      • BrainDescriptors.report_descriptors()
      • BrainDescriptors.save()
  • brainload.spatial module
    • apply_affine()
    • apply_affine_3D()
    • coords_a2s()
    • coords_s2a()
    • deg2rad()
    • get_affine_matrix_MNI152_to_MNI305()
    • get_affine_matrix_MNI305_to_MNI152()
    • get_equivalent_voxel_of_raw_volume_in_conformed_volume()
    • get_freesurfer_matrix_ras2vox()
    • get_freesurfer_matrix_vox2ras()
    • get_n_neighborhood_indices_3D()
    • get_n_neighborhood_indices_3D_points()
    • get_n_neighborhood_start_stop_indices_3D()
    • get_n_neighborhood_start_stop_indices_3D_points()
    • mirror_3D_coordinates_at_axis()
    • parse_registration_matrix()
    • point_mirror_3D_coordinates()
    • rad2deg()
    • rotate_3D_coordinates_around_axes()
    • scale_3D_coordinates()
    • translate_3D_coordinates_along_axes()
  • brainload.meshexport module
    • mesh_to_obj()
    • mesh_to_off()
    • mesh_to_ply()
    • scalars_to_colors_clist()
    • scalars_to_colors_matplotlib()
• Brainload Example Workflows
  • Loading data for a single subject
    • Load brain mesh and morphometry data for a single subject in native space
    • Load an atlas or brain parcellation for a subject (e.g., Desikan or Destrieux atlas)
    • Load morphometry data for a single subject that has been mapped to a common subject (standard space)
    • Load brain mesh and morphometry data for a group of subjects in native space
    • Load brain mesh and morphometry data for a group of subjects in standard space
    • Parse FreeSurfer stats files (e.g., aseg.stats or ?h.aparc.stats)
• Brainload Command Line Tools
  • Available command line tools
  • Getting help on command line tools

Indices and tables

• Index

• Module Index

• Search Page