Connectomics Lab Toolkit Documentation

A comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.

Installation

Install from PyPI:

conda env create -f environment.yaml
conda activate clabtoolkit-env
pip install clabtoolkit

For development installation:

git clone https://github.com/connectomicslab/clabtoolkit.git
cd clabtoolkit
pip install -e .[dev]

Quick Start

Surface Visualization

import clabtoolkit.surfacetools as cltsurf

# Reading a surface file
surf_lh = cltsurf.Surface("/opt/freesurfer/subjects/fsaverage/surf/lh.pial")

# Loading scalar maps
surf_lh.load_scalar_maps("/opt/freesurfer/subjects/fsaverage/surf/lh.thickness", maps_names="Thickness")
surf_lh.plot(overlay_name="Thickness",
            views="4_views",
            cmap= "jet",
            colorbar_position="right")

API Reference

• bidstools module
  • str2entity()
  • entity2str()
  • delete_entity()
  • replace_entity_value()
  • replace_entity_key()
  • insert_entity()
  • recursively_replace_entity_value()
  • recursively_replace_entity_key()
  • recursively_delete_entity()
  • recursively_insert_entity()
  • get_all_entities()
  • entities4table()
  • entities_to_table()
  • get_subjects()
  • copy_bids_folder()
  • get_bids_database_table()
  • get_derivatives_folders()
  • is_bids_filename()
  • get_individual_files_and_folders()
  • generate_bids_tree()
  • generate_bids_tree_with_stats()
  • validate_bids_structure()
  • load_bids_json()
  • Key Features
  • Common Usage Examples
• connectivitytools module
  • Connectome
  • Key Features
  • Main Functions
  • Common Usage Examples
• dicomtools module
  • progress_indicator()
  • org_conv_dicoms()
  • copy_dicom_file()
  • create_session_series_names()
  • uncompress_dicom_session()
  • compress_dicom_session()
  • get_dicom_info()
  • Key Features
  • Main Functions
  • Common Usage Examples
• dwitools module
  • delete_dwi_volumes()
  • get_b0s()
  • maps_from_tensor_eigenvalues()
  • DiffusionScheme
  • Key Features
  • Main Functions
  • Main Classes
  • Common Usage Examples
• freesurfertools module
  • AnnotParcellation
  • FreeSurferSubject
  • create_individual_freesurfer_table()
  • process_subject()
  • create_freesurfer_table()
  • create_fsaverage_links()
  • remove_fsaverage_links()
  • region_to_vertexwise()
  • create_vertex_colors()
  • colors2colortable()
  • resolve_colortable_duplicates()
  • find_unique_color()
  • verify_packed_rgb_values()
  • detect_hemi()
  • parse_freesurfer_lta()
  • get_cras_coordinates()
  • load_lobes_json()
  • get_version()
  • Key Features
  • Main Classes
  • Common Usage Examples
• imagetools module
  • MorphologicalOperations
  • quick_morphology()
  • get_voxel_size()
  • get_voxel_volume()
  • get_center()
  • get_rotation_matrix()
  • get_vox_neighbors()
  • crop_image_from_mask()
  • cropped_to_native()
  • apply_multi_transf()
  • vox2mm()
  • mm2vox()
  • merge_to_4d()
  • create_spams()
  • spams2maxprob()
  • simulate_image()
  • delete_volumes_from_4D_images()
  • extract_mesh_from_volume()
  • extract_centroid_from_volume()
  • create_spams_from_volume()
  • spams2maxprob_from_volume()
  • compute_statistics_at_nonzero_voxels()
  • interpolate()
  • region_growing()
  • simulate_array()
  • delete_volumes_from_4D_array()
  • dilate_mm()
  • Key Features
  • Main Classes
  • Common Usage Examples
• misctools module
  • ExplorerDict
  • update_dict()
  • Key Features
  • Main Classes
  • Common Usage Examples
• morphometrytools module
  • compute_reg_val_fromannot()
  • compute_reg_area_fromsurf()
  • compute_reg_nvertices_fromsurf()
  • compute_euler_fromsurf()
  • area_from_mesh()
  • euler_from_mesh()
  • compute_reg_val_fromparcellation()
  • compute_reg_volume_fromparcellation()
  • parse_freesurfer_global_fromaseg()
  • parse_freesurfer_stats_fromaseg()
  • parse_freesurfer_cortex_stats()
  • get_stats_dictionary()
  • network_metrics_to_table()
  • stats_from_vector()
  • get_units()
  • Key Features
  • Main Functions
  • Common Usage Examples
• networktools module
  • adjacency_matrix_to_csr()
  • triangulated_mesh_to_csr()
  • edges_to_csr()
  • edges_to_components()
  • connected_components()
  • Key Features
  • Main Functions
  • Common Usage Examples
• parcellationtools module
  • Parcellation
  • RegionTimeSeries
  • Key Features
  • Main Classes
  • Common Usage Examples
• pipelinetools module
  • get_ids2process()
  • create_processing_status_table()
  • process_file()
  • process_freesurfer_subject()
  • scan_derivatives()
  • build_inventory()
  • build_derivatives_inventory()
  • get_processing_status_details_json()
  • get_processing_status_details_sqlite3()
  • query_processing_status_db()
  • export_db_to_json()
  • Key Features
  • Main Functions
  • Common Usage Examples
• plottools module
  • get_screen_size()
  • get_current_monitor_size()
  • estimate_monitor_dpi()
  • calculate_optimal_subplots_grid()
  • calculate_subplot_layout()
  • create_proportional_subplots()
  • calculate_font_sizes()
  • get_pyvista_fonts()
  • Key Features
  • Main Functions
  • Common Usage Examples
• qcqatools module
  • get_valid_slices()
  • generate_slices()
  • recursively_generate_slices()
  • generate_image_selection_webpage()
  • create_png_webpage_from_generated_slices()
  • Key Features
  • Main Functions
  • Common Usage Examples
• segmentationtools module
  • abased_parcellation()
  • tissue_seg_table()
  • Key Features
  • Main Functions
  • Common Usage Examples
• surfacetools module
  • Surface
  • merge_surfaces()
  • create_surface_colortable()
  • Key Features
  • Main Classes
  • Common Usage Examples
• visualizationtools module
  • BrainPlotter
  • create_carpet_plot()
  • Key Features
  • Main Classes
  • Common Usage Examples

Indices and tables

• Index

• Module Index

• Search Page