toolbox_folders.md

CanlabCore folder map

This page lists the directories under CanlabCore/ and what each one contains. The toolbox is a flat collection of folders rather than packaged MATLAB modules; running canlab_toolbox_setup adds them all to your path.

Class folders

These are MATLAB class folders (@<classname>/). Each contains the class definition and the methods you can call on instances of that class. See Object_methods.md for the cross-cutting documentation index.

Folder	Class	Purpose
@image_vector/	image_vector	Abstract base class for objects that hold image data as [voxels x images]. Most other image classes inherit from it.
@fmri_data/	fmri_data	Workhorse class for fMRI / PET / contrast images. Adds .X, .Y, .covariates, prediction, regression, ICA, etc.
@statistic_image/	statistic_image	Stat maps with t / p / effect-size values, with thresholding state.
@atlas/	atlas	Brain atlases / parcellations with probability maps and labels.
@region/	region	Lists of contiguous clusters / ROIs as a unit of analysis.
@fmridisplay/	fmridisplay	Container holding handles for slice montages and surfaces, used to keep figure layers around for blob editing.
@brainpathway/	brainpathway	Connectivity / pathway-modeling object for one subject.
@brainpathway_multisubject/	brainpathway_multisubject	Group-level extension of brainpathway for many subjects.
@fmri_timeseries/	fmri_timeseries	Specialized container for raw timeseries data.
@canlab_dataset/	canlab_dataset	Generic subject x variable behavioral / clinical data container.
@fmri_glm_design_matrix/	fmri_glm_design_matrix	Design matrix container for first-level GLMs.
@predictive_model/	predictive_model	Holds artifacts of a fitted multivariate prediction model.
@fmri_mask_image/	fmri_mask_image	Binary mask container (legacy; many newer methods accept fmri_data or image_vector directly).

Function library folders

Folder	Purpose
canlab_canonical_brains/	Canonical underlay images, surface meshes, and standard masks (gray-matter, white-matter, ventricles, brainmask). Used by montage, surface, extract_gray_white_csf, etc.
Cifti_plotting/	Tools to read CIFTI dlabel files and render data on surfaces. Includes render_cifti_on_brain, cifti_struct_2_region_obj, make_surface_figure.
Cluster_contig_region_tools/	Tools for finding, merging, and labeling contiguous clusters in image volumes. The bridge between voxelwise stat maps and region-object outputs.
Data_extraction/	Loaders and ROI extraction. Includes load_atlas, load_image_set, canlab_load_ROI, extract_image_data, extract_from_rois.
Data_processing_tools/	Timeseries filtering, FFT, distance matrices, mean imputation, and similar low-level helpers (e.g., hpfilter, canlab_compute_similarity_matrix, canlab_extract_ventricle_wm_timeseries).
diagnostics/	Quality-control and image-diagnostic functions: canlab_qc_metrics1, scnlab_norm_check, intensity histograms, image effect-size maps.
External/	Vendored third-party toolboxes (matlab_bgl, spider, lasso, BCT, umap, export_fig, boundedline, etc.). Generally treat as read-only.
Filename_tools/	Filename and BIDS helpers: canlab_list_files, canlab_list_subjects, extract_bids_info, expand_4d_filenames, gunzip_image_names_if_gz.
fmridisplay_helper_functions/	Internal helpers used by @fmridisplay to lay out, color, and update slice / surface views.
GLM_Batch_tools/	SPM-driven first- and second-level GLM batch system. Driven by a DSGN struct; see canlab_glm_subject_levels, canlab_glm_group_levels, canlab_glm_README.txt.
hewma_utility/	Hierarchical Exponentially Weighted Moving Average change-point analysis utilities for fMRI timeseries.
HRF_Est_Toolbox4/	HRF estimation (canonical + temporal / dispersion derivatives, FIR / smooth FIR, IL-model, NL-gamma, splines).
Image_computation_tools/	Voxelwise computation utilities used by methods (e.g., image_eval_function, image_eval_function_multisubj, mean_image, scn_num_volumes, scn_write_plane, tor_global).
Image_space_tools/	Reslicing and voxel-space transformations (e.g., mat2voxel, mm2voxel, voxel2mm, scn_map_image).
Image_thresholding/	Statistical thresholding utilities (FDR, cluster-extent thresholds, GRF, clusterSizeMask).
Index_image_manip_tools/	The iimg_* family — internal index-image / volInfo manipulation that backs many class methods (iimg_read_img, iimg_get_data, iimg_reconstruct_vols, iimg_reslice, etc.).
Misc_utilities/	General-purpose helpers and the canonical documentation_template.m. Includes things that don't fit elsewhere — framewise_displacement, canlab_print_legend_text, etc.
mlpcr/	Multi-level Principal Component Regression, used as a predict algorithm option.
Model_building_tools/	First-level GLM design construction: onsets2fmridesign, getPredictors, create_random_er_design, fmri_spline_basis, basis-set tools.
OptimizeDesign11/	Genetic-algorithm fMRI experimental-design optimization.
Parcellation_tools/	Parcellation utilities: cluster solutions, splitting / merging parcels, parcel-wise summary.
peak_coordinates/	Peak coordinate detection and extraction (tal_pos_neg, peak utilities).
Reporting/	Reporting helpers for analysis output (e.g., summarize_regression).
ROI_drawing_tools/	Interactive ROI drawing utilities.
Sample_datasets/	Small test fixtures shipped with the toolbox: Wager 2008 EmotionReg contrasts, Pinel localizer timeseries, Jepma single-trial dataset, Woo 2015 BMRK3 pain, Atlas 2012 REMI behavioral. See sample_datasets.md.
Statistics_tools/	Statistical functions: correlation, glmfit_*, classifiers, bootstrap, FDR, mediation helpers, igls, predictor selection, etc.
Unit_tests/	The matlab.unittest-based test suite. Run with canlab_run_all_tests. See Unit_tests/README.md.
Visualization_functions/	The plotting library: barplot_columns, addbrain, canlab_results_fmridisplay, canlab_canonical_brain_surface_cutaways, color maps, histogram tools, etc.
web_repository_tools/	Helpers to clone, update, and sync the CANlab GitHub repositories (e.g., canlab_clone_github_repository).

Top-level files

File	Purpose
canlab_toolbox_setup.m	Entry-point script users run from the directory above their CANlab clones; finds and adds CanlabCore + sibling repos to the MATLAB path.
canlab_clone_github_repository.m	Helper for canlab_toolbox_setup; clones missing CANlab repos.
fmri_data_methods.md	Cross-cutting functional index of @fmri_data + @image_vector methods (lives at the toolbox root, not in docs/).
poorly_documented_functions.txt	Ranked survey of files whose help blocks differ from the documentation template; used to scope docstring rewrites.