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CanlabCore
This repository contains core tools for MRI/fMRI/PET analysis from the Cognitive and Affective Neuorscience Lab (Tor Wager, PI) and our collaborators. The tools provide a high-level language for interacting with neuroimaging data. The idea is to take preprocessed data or even the results of single-subject analyses—the output of established preprocessing pipelines—and import them into lightweight, flexible data objects specialized for neuroimaging visualization and analysis. These objects allow for interactive analysis with simple commands, like “plot”, “predict”, and “montage”. The repository also includes other useful toolboxes, including fMRI design optimization using a genetic algorithm, fMRI HRF estimation, fMRI analysis with Hierarchical Exponentially Weighted Moving Average change-point analysis, various fMRI diagnostics, and miscellaneous other tools and functions for visualizing brain data.
Cite As
Tor Wager (2024). CanlabCore (https://github.com/canlab/CanlabCore), GitHub. Retrieved .
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- Sciences > Neuroscience > Human Brain Mapping > MRI >
- Engineering > Biomedical Engineering > Biomedical Imaging >
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CanlabCore
- canlab_clone_github_repository
- canlab_clone_github_repository
- canlab_toolbox_setup
- canlab_toolbox_setup
CanlabCore/@atlas
- atlas
- atlas
- atlas2region
- atlas2region
- atlas_add_L_R_to_labels
- atlas_add_L_R_to_labels
- atlas_get_probability_maps
- atlas_get_probability_maps
- atlas_similarity
- atlas_similarity
- check_properties
- check_properties
- create
- create
- downsample_parcellation
- downsample_parcellation
- extract_data
- extract_data
- find_closest_region
- find_closest_region
- get_region_volumes
- get_region_volumes
- horzcat
- horzcat
- isosurface
- isosurface
- merge_atlases
- merge_atlases
- montage
- montage
- num_regions
- num_regions
- parcel_data2fmri_data
- parcel_data2fmri_data
- parcel_stats2statistic_image
- parcel_stats2statistic_image
- probability_maps_to_region_index
- probability_maps_to_region_index
- remove_atlas_region
- remove_atlas_region
- reorder_atlas_regions
- reorder_atlas_regions
- select_atlas_subset
- select_atlas_subset
- select_regions_near_crosshairs
- select_regions_near_crosshairs
- split_atlas_by_hemisphere
- split_atlas_by_hemisphere
- split_atlas_into_contiguous_regions
- split_atlas_into_contiguous_regions
- threshold
- threshold
CanlabCore/@brainpathway
- attach_voxel_data.m
- attach_voxel_data.m
- brainpathway
- brainpathway
- brainpathway2fmri_data
- brainpathway2fmri_data
- degree_calc
- degree_calc
- find_node_indices
- find_node_indices
- nan2zero
- nan2zero
- reorder_regions_by_node_cluster
- reorder_regions_by_node_cluster
- seed_connectivity
- seed_connectivity
- threshold_connectivity
- threshold_connectivity
CanlabCore/@brainpathway/private
CanlabCore/@brainpathway_multisubject
- bct_toolbox_undirected_graph_metrics
- bct_toolbox_undirected_graph_metrics
- brainpathway_multisubject
- brainpathway_multisubject
- compute_HDIs
- compute_HDIs
- flatten_conn_matrices
- flatten_conn_matrices
- get_wh_subjects
- get_wh_subjects
- ISC
- ISC
- qcfc
- qcfc
- ttest
- ttest
CanlabCore/@canlab_dataset
- add_vars
- add_vars
- bars
- bars
- canlab_dataset
- canlab_dataset
- concatenate
- concatenate
- get_descriptives
- get_descriptives
- get_var
- get_var
- glm
- glm
- glm_multilevel
- glm_multilevel
- histogram
- histogram
- list_variables
- list_variables
- mediation
- mediation
- plot_var
- plot_var
- print_summary
- print_summary
- read_from_excel
- read_from_excel
- reliability
- reliability
- replace_values
- replace_values
- scattermatrix
- scattermatrix
- scatterplot
- scatterplot
- scatterplot
- scatterplot
- select_trials_and_subjects
- select_trials_and_subjects
- spm2canlab_dataset
- spm2canlab_dataset
- ttest2
- ttest2
- write_text
- write_text
CanlabCore/@fmri_data
- bootstrap_structure_coeff_diff
- bootstrap_structure_coeff_diff
- canlab_connectivity_preproc
- canlab_connectivity_preproc
- cat
- cat
- create
- create
- evaluate_spatial_scale
- evaluate_spatial_scale
- extract_measures_batch
- extract_measures_batch
- extract_roi_averages
- extract_roi_averages
- fmri_data
- fmri_data
- horzcat
- horzcat
- hrf_fit
- hrf_fit
- model_brain_pathway
- model_brain_pathway
- neurosynth_feature_labels
- neurosynth_feature_labels
- plot
- plot
- predict
- predict
- predict_test_suite
- predict_test_suite
- regress
- regress
- rescale
- rescale
- riverplot
- riverplot
- robfit_parcelwise
- robfit_parcelwise
- rsa_regression
- rsa_regression
- saveplots
- saveplots
- signtest
- signtest
- sim_data
- sim_data
- split
- split
- spm_coregister
- spm_coregister
- structure_coefficient_map
- structure_coefficient_map
- test_generalizability
- test_generalizability
- ttest
- ttest
- ttest_table_and_lateralization_test
- ttest_table_and_lateralization_test
- windsorize
- windsorize
CanlabCore/@fmri_glm_design_matrix
- add
- add
- Add_Event_Info
- Add_Event_Info
- build
- build
- build_single_trial
- build_single_trial
- fmri_glm_design_matrix
- fmri_glm_design_matrix
- get_condition_assignments
- get_condition_assignments
- get_session_X
- get_session_X
- import_onsets
- import_onsets
- plot
- plot
- replace_basis_set
- replace_basis_set
- robustfit
- robustfit
- rotate_to_pca
- rotate_to_pca
- saveplots
- saveplots
- single_trial_estimates
- single_trial_estimates
CanlabCore/@fmri_mask_image
CanlabCore/@fmri_timeseries
CanlabCore/@fmridisplay
- activate_figures
- activate_figures
- addblobs
- addblobs
- addpoints
- addpoints
- addthreshblobs
- addthreshblobs
- fmridisplay
- fmridisplay
- legend
- legend
- montage
- montage
- removeblobs
- removeblobs
- removepoints
- removepoints
- surface
- surface
- title_montage
- title_montage
- transparency_change
- transparency_change
- zoom_in_on_regions
- zoom_in_on_regions
CanlabCore/@image_vector
- apply_atlas
- apply_atlas
- apply_mask
- apply_mask
- apply_parcellation
- apply_parcellation
- check_image_filenames
- check_image_filenames
- compare_space
- compare_space
- descriptives
- descriptives
- display_slices
- display_slices
- enforce_variable_types
- enforce_variable_types
- expand_into_atlas_subregions.m
- expand_into_atlas_subregions.m
- extract_gray_white_csf
- extract_gray_white_csf
- extract_roi_averages
- extract_roi_averages
- flip
- flip
- get_wh_image
- get_wh_image
- get_xyzmm_coordinates
- get_xyzmm_coordinates
- hansen_neurotransmitter_maps
- hansen_neurotransmitter_maps
- histogram
- histogram
- history
- history
- horzcat
- horzcat
- ica
- ica
- image_math
- image_math
- image_similarity_plot
- image_similarity_plot
- image_similarity_plot_bucknermaps
- image_similarity_plot_bucknermaps
- image_vector
- image_vector
- interpolate
- interpolate
- isempty
- isempty
- isosurface
- isosurface
- mahal
- mahal
- mean
- mean
- minus
- minus
- montage
- montage
- orthviews
- orthviews
- outliers
- outliers
- outliers_xval
- outliers_xval
- pattern_surf_plot_mip
- pattern_surf_plot_mip
- pca
- pca
- plot_current_orthviews_coord
- plot_current_orthviews_coord
- plus
- plus
- power
- power
- prctile
- prctile
- preprocess
- preprocess
- qc_metrics_second_level
- qc_metrics_second_level
- read_from_file
- read_from_file
- rebuild_volinfo_from_dat
- rebuild_volinfo_from_dat
- reconstruct_image
- reconstruct_image
- remove_empty
- remove_empty
- render_on_surface
- render_on_surface
- reparse_contiguous
- reparse_contiguous
- replace_empty
- replace_empty
- resample_space
- resample_space
- resample_time
- resample_time
- rmssd_movie
- rmssd_movie
- searchlight
- searchlight
- searchlightLukas
- searchlightLukas
- select_voxels_by_value
- select_voxels_by_value
- slices
- slices
- slice_movie
- slice_movie
- subdivide_by_atlas
- subdivide_by_atlas
- surface
- surface
- table
- table
- table_of_atlas_regions_covered
- table_of_atlas_regions_covered
- threshold
- threshold
- trim_mask
- trim_mask
- union
- union
- unstack_by_condition
- unstack_by_condition
- wedge_plot_by_atlas
- wedge_plot_by_atlas
- write
- write
CanlabCore/@predictive_model
CanlabCore/@region
- autolabel_regions_using_atlas
- autolabel_regions_using_atlas
- check_extracted_data
- check_extracted_data
- extract_data
- extract_data
- isempty
- isempty
- isosurface
- isosurface
- match_colors_left_right
- match_colors_left_right
- merge
- merge
- montage
- montage
- orthviews
- orthviews
- posneg_separate
- posneg_separate
- region
- region
- region2atlas
- region2atlas
- region2fmri_data
- region2fmri_data
- region2imagevec
- region2imagevec
- region2imagevec
- region2imagevec
- region2imagevec2tmp
- region2imagevec2tmp
- region2struct
- region2struct
- reparse_continguous
- reparse_continguous
- select_coordinates_near_regions
- select_coordinates_near_regions
- subdivide_by_atlas
- subdivide_by_atlas
- subdivide_by_local_max
- subdivide_by_local_max
- surface
- surface
- table
- table
- table_of_atlas_regions_covered
- table_of_atlas_regions_covered
- table_simple
- table_simple
- ttest_table_by_condition
- ttest_table_by_condition
CanlabCore/@statistic_image
- check_properties
- check_properties
- conjunction
- conjunction
- convert2mask
- convert2mask
- estimateBayesFactor
- estimateBayesFactor
- multi_threshold
- multi_threshold
- orthviews
- orthviews
- reparse_contiguous
- reparse_contiguous
- riverplot
- riverplot
- select_one_image
- select_one_image
- statistic_image
- statistic_image
- table
- table
- threshold
- threshold
CanlabCore/Cifti_plotting
- make_surface_figure
- make_surface_figure
- plot_surface_map
- plot_surface_map
- read_dlabel_cifti
- read_dlabel_cifti
- surface_outlines
- surface_outlines
CanlabCore/Cluster_contig_region_tools
- anat_subclusters
- anat_subclusters
- cluster2region
- cluster2region
- cluster2subclusters
- cluster2subclusters
- clusters2CLU
- clusters2CLU
- clusters2mask
- clusters2mask
- cluster_close_enough
- cluster_close_enough
- cluster_export_pngs
- cluster_export_pngs
- cluster_find_index
- cluster_find_index
- cluster_interp
- cluster_interp
- cluster_intersection
- cluster_intersection
- cluster_local_maxima
- cluster_local_maxima
- cluster_set_intersection
- cluster_set_intersection
- cluster_table
- cluster_table
- cluster_table_old
- cluster_table_old
- cluster_table_successive_threshold
- cluster_table_successive_threshold
- enlarge_cluster
- enlarge_cluster
- image2clusters
- image2clusters
- mask2clusters
- mask2clusters
- mask2struct
- mask2struct
- merge_clusters
- merge_clusters
- merge_nearby_clusters
- merge_nearby_clusters
- subclusters_from_local_max
- subclusters_from_local_max
- xyz2clusters
- xyz2clusters
CanlabCore/Cluster_contig_region_tools/Cluster-based_multivar_tools
- cluster_discrim
- cluster_discrim
- cluster_discrim_montage
- cluster_discrim_montage
- cluster_FA
- cluster_FA
- cluster_network
- cluster_network
- cluster_nmdsfig
- cluster_nmdsfig
- cluster_nmdsfig_glassbrain
- cluster_nmdsfig_glassbrain
- cluster_princomp
- cluster_princomp
- cluster_princomp2
- cluster_princomp2
- discrim_plot
- discrim_plot
- nmdsfig_tools
- nmdsfig_tools
- partialcor
- partialcor
CanlabCore/Cluster_contig_region_tools/Cluster_based_statistics
- cluster_names
- cluster_names
- cluster_sigregions
- cluster_sigregions
- cluster_sigregions
- cluster_sigregions
- cluster_ttest
- cluster_ttest
- npm_ttest
- npm_ttest
CanlabCore/Cluster_contig_region_tools/cluster_tool
- adjacent_test
- adjacent_test
- check_cl
- check_cl
- cluster_tool
- cluster_tool
- cluster_tool_append
- cluster_tool_append
- cluster_tool_callgui
- cluster_tool_callgui
- cluster_tool_draw_sphere
- cluster_tool_draw_sphere
- cluster_tool_edit
- cluster_tool_edit
- cluster_tool_getbetas
- cluster_tool_getbetas
- cluster_tool_getver
- cluster_tool_getver
- cluster_tool_maskq
- cluster_tool_maskq
- cluster_tool_masktypeq
- cluster_tool_masktypeq
- cluster_tool_savefunc.m
- cluster_tool_savefunc.m
- cluster_tool_subdivide
- cluster_tool_subdivide
- cluster_tool_table
- cluster_tool_table
- cluster_tool_thresh
- cluster_tool_thresh
- cluster_tool_tools
- cluster_tool_tools
- cluster_tool_writemasktypeq
- cluster_tool_writemasktypeq
- cl_cl_intersect
- cl_cl_intersect
- cl_img_intersect
- cl_img_intersect
- cl_subdivide
- cl_subdivide
- mmToVoxel
- mmToVoxel
- space_match
- space_match
- sphere_3d
- sphere_3d
- voxelToMm
- voxelToMm
CanlabCore/Data_extraction
- canlab_load_ROI
- canlab_load_ROI
- canlab_maskstats
- canlab_maskstats
- cluster_tmask
- cluster_tmask
- extract_contrast_data
- extract_contrast_data
- extract_from_rois
- extract_from_rois
- extract_image_data
- extract_image_data
- extract_indiv_peak_data
- extract_indiv_peak_data
- extract_raw_data
- extract_raw_data
- load_atlas
- load_atlas
- load_image_set
- load_image_set
- readim2
- readim2
- read_hdr
- read_hdr
- sphere_roi_tool_2008
- sphere_roi_tool_2008
- sphere_roi_tool_2008_conflict.m
- sphere_roi_tool_2008_conflict.m
- timeseries_extract_slice
- timeseries_extract_slice
- tor_extract_rois
- tor_extract_rois
CanlabCore/Data_extraction/DataHash_20190519
CanlabCore/Data_extraction/Grandfathered
CanlabCore/Data_extraction/read_gzip_nii
CanlabCore/Data_processing_tools
- canlab_extract_ventricle_wm_timeseries
- canlab_extract_ventricle_wm_timeseries
- center_of_mass
- center_of_mass
- correlation_2d_to_3d
- correlation_2d_to_3d
- correlation_3d_to_2d
- correlation_3d_to_2d
- detransition
- detransition
- downsample_scnlab
- downsample_scnlab
- fft_plot_scnlab
- fft_plot_scnlab
- filterAdjust
- filterAdjust
- fir2htw2
- fir2htw2
- get_snr
- get_snr
- hpfilter
- hpfilter
- htw_from_fit
- htw_from_fit
- luisFilter
- luisFilter
- nuisance_cov_estimates
- nuisance_cov_estimates
- physio_data
- physio_data
- rankdata
- rankdata
- resample_scnlab
- resample_scnlab
- scale
- scale
- scnlab_filter_fmri_data
- scnlab_filter_fmri_data
- scnlab_outlier_id
- scnlab_outlier_id
- selective_average
- selective_average
- selective_average_group
- selective_average_group
- smooth_timeseries
- smooth_timeseries
- splineDetrend
- splineDetrend
- splinetrim
- splinetrim
- struct2canlab_dataset
- struct2canlab_dataset
- table2canlab_dataset
- table2canlab_dataset
- table_long2wide
- table_long2wide
- trimts
- trimts
- use_spm_filter
- use_spm_filter
CanlabCore/External/2019_03_03_BCT
- adjacency_plot_und
- adjacency_plot_und
- agreement
- agreement
- agreement_weighted
- agreement_weighted
- align_matrices
- align_matrices
- assortativity_bin
- assortativity_bin
- assortativity_wei
- assortativity_wei
- backbone_wu
- backbone_wu
- betweenness_bin
- betweenness_bin
- betweenness_wei
- betweenness_wei
- breadth
- breadth
- breadthdist
- breadthdist
- charpath
- charpath
- clique_communities
- clique_communities
- clustering_coef_bd
- clustering_coef_bd
- clustering_coef_bu
- clustering_coef_bu
- clustering_coef_wd
- clustering_coef_wd
- clustering_coef_wu
- clustering_coef_wu
- clustering_coef_wu_sign
- clustering_coef_wu_sign
- community_louvain
- community_louvain
- consensus_und
- consensus_und
- core_periphery_dir
- core_periphery_dir
- cycprob
- cycprob
- degrees_dir
- degrees_dir
- degrees_und
- degrees_und
- density_dir
- density_dir
- density_und
- density_und
- diffusion_efficiency
- diffusion_efficiency
- distance_bin
- distance_bin
- distance_wei
- distance_wei
- distance_wei_floyd
- distance_wei_floyd
- diversity_coef_sign
- diversity_coef_sign
- edge_betweenness_bin
- edge_betweenness_bin
- edge_betweenness_wei
- edge_betweenness_wei
- edge_nei_overlap_bd
- edge_nei_overlap_bd
- edge_nei_overlap_bu
- edge_nei_overlap_bu
- efficiency_bin
- efficiency_bin
- efficiency_wei
- efficiency_wei
- eigenvector_centrality_und
- eigenvector_centrality_und
- erange
- erange
- evaluate_generative_model
- evaluate_generative_model
- findpaths
- findpaths
- findwalks
- findwalks
- find_motif34
- find_motif34
- flow_coef_bd
- flow_coef_bd
- gateway_coef_sign
- gateway_coef_sign
- generate_fc
- generate_fc
- generative_model
- generative_model
- get_components
- get_components
- grid_communities
- grid_communities
- gtom
- gtom
- jdegree
- jdegree
- kcoreness_centrality_bd
- kcoreness_centrality_bd
- kcoreness_centrality_bu
- kcoreness_centrality_bu
- kcore_bd
- kcore_bd
- kcore_bu
- kcore_bu
- latmio_dir
- latmio_dir
- latmio_dir_connected
- latmio_dir_connected
- latmio_und
- latmio_und
- latmio_und_connected
- latmio_und_connected
- link_communities
- link_communities
- local_assortativity_wu_sign
- local_assortativity_wu_sign
- makeevenCIJ
- makeevenCIJ
- makefractalCIJ
- makefractalCIJ
- makelatticeCIJ
- makelatticeCIJ
- makerandCIJdegreesfixed
- makerandCIJdegreesfixed
- makerandCIJ_dir
- makerandCIJ_dir
- makerandCIJ_und
- makerandCIJ_und
- makeringlatticeCIJ
- makeringlatticeCIJ
- maketoeplitzCIJ
- maketoeplitzCIJ
- make_motif34lib
- make_motif34lib
- matching_ind
- matching_ind
- matching_ind_und
- matching_ind_und
- mean_first_passage_time
- mean_first_passage_time
- mleme_constraint_model
- mleme_constraint_model
- modularity_dir
- modularity_dir
- modularity_und
- modularity_und
- module_degree_zscore
- module_degree_zscore
- motif3funct_bin
- motif3funct_bin
- motif3funct_wei
- motif3funct_wei
- motif3struct_bin
- motif3struct_bin
- motif3struct_wei
- motif3struct_wei
- motif4funct_bin
- motif4funct_bin
- motif4funct_wei
- motif4funct_wei
- motif4struct_bin
- motif4struct_bin
- motif4struct_wei
- motif4struct_wei
- navigation_wu
- navigation_wu
- null_model_dir_sign
- null_model_dir_sign
- null_model_und_sign
- null_model_und_sign
- pagerank_centrality
- pagerank_centrality
- participation_coef
- participation_coef
- participation_coef_sign
- participation_coef_sign
- partition_distance
- partition_distance
- path_transitivity
- path_transitivity
- predict_fc
- predict_fc
- quasi_idempotence
- quasi_idempotence
- randmio_dir
- randmio_dir
- randmio_dir_connected
- randmio_dir_connected
- randmio_dir_signed
- randmio_dir_signed
- randmio_und
- randmio_und
- randmio_und_connected
- randmio_und_connected
- randmio_und_signed
- randmio_und_signed
- randomizer_bin_und
- randomizer_bin_und
- randomize_graph_partial_und
- randomize_graph_partial_und
- reachdist
- reachdist
- rentian_scaling_2d
- rentian_scaling_2d
- rentian_scaling_3d
- rentian_scaling_3d
- reorderMAT
- reorderMAT
- reorder_matrix
- reorder_matrix
- reorder_mod
- reorder_mod
- resource_efficiency_bin
- resource_efficiency_bin
- retrieve_shortest_path
- retrieve_shortest_path
- rich_club_bd
- rich_club_bd
- rich_club_bu
- rich_club_bu
- rich_club_wd
- rich_club_wd
- rich_club_wu
- rich_club_wu
- rout_efficiency
- rout_efficiency
- score_wu
- score_wu
- search_information
- search_information
- strengths_dir
- strengths_dir
- strengths_und
- strengths_und
- strengths_und_sign
- strengths_und_sign
- subgraph_centrality
- subgraph_centrality
- threshold_absolute
- threshold_absolute
- threshold_proportional
- threshold_proportional
- transitivity_bd
- transitivity_bd
- transitivity_bu
- transitivity_bu
- transitivity_wd
- transitivity_wd
- transitivity_wu
- transitivity_wu
- weight_conversion
- weight_conversion
- writetoPAJ
- writetoPAJ
CanlabCore/External/2019_03_03_BCT/data_and_demos
- demo_efficiency_measures.m
- demo_efficiency_measures.m
- demo_generative_models_geometric.m
- demo_generative_models_geometric.m
- demo_generative_models_neighbors.m
- demo_generative_models_neighbors.m
CanlabCore/External/BF
CanlabCore/External/boundedline
CanlabCore/External/boundedline/Inpaint_nans
CanlabCore/External/boundedline/Inpaint_nans/demo
CanlabCore/External/boundedline/Inpaint_nans/doc
CanlabCore/External/boundedline/Inpaint_nans/test
CanlabCore/External/boundedline/boundedline
CanlabCore/External/boundedline/catuneven
CanlabCore/External/boundedline/singlepatch
CanlabCore/External/circularGraph
CanlabCore/External/export_fig
- append_pdfs.m
- append_pdfs.m
- copyfig
- copyfig
- crop_borders
- crop_borders
- eps2pdf
- eps2pdf
- export_fig
- export_fig
- fix_lines.m
- fix_lines.m
- ghostscript
- ghostscript
- im2gif.m
- im2gif.m
- isolate_axes
- isolate_axes
- pdf2eps.m
- pdf2eps.m
- pdftops
- pdftops
- print2array
- print2array
- print2eps
- print2eps
- read_write_entire_textfile.m
- read_write_entire_textfile.m
- user_string
- user_string
- using_hg2.m
- using_hg2.m
CanlabCore/External/lasso
- lasso_coefficients
- lasso_coefficients
- lasso_cv
- lasso_cv
- lasso_predict
- lasso_predict
- lasso_rocha
- lasso_rocha
- lasso_selection
- lasso_selection
- penalized_coefficients
- penalized_coefficients
- plot_duals_example.m
- plot_duals_example.m
CanlabCore/External/lasso/tests
CanlabCore/External/matlab_bgl
- all_shortest_paths
- all_shortest_paths
- astar_search
- astar_search
- bellman_ford_sp
- bellman_ford_sp
- betweenness_centrality
- betweenness_centrality
- bfs
- bfs
- biconnected_components
- biconnected_components
- boyer_myrvold_planarity_test
- boyer_myrvold_planarity_test
- breadth_first_search
- breadth_first_search
- chrobak_payne_straight_line_drawing
- chrobak_payne_straight_line_drawing
- circle_graph_layout
- circle_graph_layout
- clique_graph
- clique_graph
- clustering_coefficients
- clustering_coefficients
- combine_visitors
- combine_visitors
- components
- components
- Contents.m
- Contents.m
- core_numbers
- core_numbers
- cycle_graph
- cycle_graph
- dag_sp
- dag_sp
- depth_first_search
- depth_first_search
- dfs
- dfs
- dijkstra_sp
- dijkstra_sp
- edge_weight_index
- edge_weight_index
- edge_weight_vector
- edge_weight_vector
- edmonds_maximum_cardinality_matching
- edmonds_maximum_cardinality_matching
- edmunds_karp_max_flow
- edmunds_karp_max_flow
- erdos_reyni
- erdos_reyni
- floyd_warshall_all_sp
- floyd_warshall_all_sp
- fruchterman_reingold_force_directed_layout
- fruchterman_reingold_force_directed_layout
- grid_graph
- grid_graph
- gursoy_atun_layout
- gursoy_atun_layout
- indexed_sparse
- indexed_sparse
- is_kuratowski_graph
- is_kuratowski_graph
- is_straight_line_drawing
- is_straight_line_drawing
- johnson_all_sp
- johnson_all_sp
- kamada_kawai_spring_layout
- kamada_kawai_spring_layout
- kolmogorov_max_flow
- kolmogorov_max_flow
- kruskal_mst
- kruskal_mst
- kuratowski_subgraph
- kuratowski_subgraph
- lengauer_tarjan_dominator_tree
- lengauer_tarjan_dominator_tree
- make_biconnected_planar
- make_biconnected_planar
- make_connected
- make_connected
- make_maximal_planar
- make_maximal_planar
- matching
- matching
- maximal_matching
- maximal_matching
- max_flow
- max_flow
- mst
- mst
- num_edges
- num_edges
- num_vertices
- num_vertices
- path_from_pred
- path_from_pred
- planar_canonical_ordering
- planar_canonical_ordering
- prim_mst
- prim_mst
- push_relabel_max_flow
- push_relabel_max_flow
- random_graph_layout
- random_graph_layout
- set_matlab_bgl_default
- set_matlab_bgl_default
- shortest_paths
- shortest_paths
- star_graph
- star_graph
- test_dag
- test_dag
- test_matching
- test_matching
- test_planar_graph
- test_planar_graph
- topological_order
- topological_order
- tree_from_pred
- tree_from_pred
- wheel_graph
- wheel_graph
CanlabCore/External/matlab_bgl/@inplace
- assign
- assign
- display
- display
- double
- double
- end
- end
- inplace
- inplace
- size
- size
- subsasgn
- subsasgn
- subsref
- subsref
CanlabCore/External/matlab_bgl/@ipdouble
CanlabCore/External/matlab_bgl/@ipint32
CanlabCore/External/matlab_bgl/custom
CanlabCore/External/matlab_bgl/doc
CanlabCore/External/matlab_bgl/examples
- approx_multiway_cut
- approx_multiway_cut
- bacon_numbers
- bacon_numbers
- bfs_example.m
- bfs_example.m
- bfs_in_mbgl
- bfs_in_mbgl
- bfs_in_mbgl
- bfs_in_mbgl
- core_numbers_example.m
- core_numbers_example.m
- dfs_example.m
- dfs_example.m
- edge_index_example.m
- edge_index_example.m
- max_flow_example.m
- max_flow_example.m
- multiway_example.m
- multiway_example.m
- new_in_3_0.m
- new_in_3_0.m
- new_in_4_0.m
- new_in_4_0.m
- planar_graphs.m
- planar_graphs.m
- record_alg.m
- record_alg.m
- red_black.m
- red_black.m
- reweighted_graphs.m
- reweighted_graphs.m
CanlabCore/External/matlab_bgl/private
- check_matlab_bgl
- check_matlab_bgl
- compile
- compile
- get_matlab_bgl_options
- get_matlab_bgl_options
- merge_options
- merge_options
- merge_structs
- merge_structs
- todo.m
- todo.m
- todo_3_0_release.m
- todo_3_0_release.m
CanlabCore/External/matlab_bgl/test
- canlab_assert
- canlab_assert
- rtest_1
- rtest_1
- rtest_2
- rtest_2
- rtest_3_cojocaru
- rtest_3_cojocaru
- rtest_5_henderson
- rtest_5_henderson
- rtest_6
- rtest_6
- rtest_7_karsi
- rtest_7_karsi
- rtest_all.m
- rtest_all.m
- test_all.m
- test_all.m
- test_benchmark
- test_benchmark
- test_breadth_first_search
- test_breadth_first_search
- test_components
- test_components
- test_depth_first_search
- test_depth_first_search
- test_examples
- test_examples
- test_layouts
- test_layouts
- test_main
- test_main
- test_planar.m
- test_planar.m
- test_searches.m
- test_searches.m
- test_shortest_paths
- test_shortest_paths
- test_spanning_trees
- test_spanning_trees
- test_statistics
- test_statistics
- test_trivial.m
- test_trivial.m
CanlabCore/External/spider
- Contents.m
- Contents.m
- spider_init.m
- spider_init.m
- spider_path
- spider_path
- spider_subdirs
- spider_subdirs
- use_spider
- use_spider
CanlabCore/External/spider/Optimization
- Contents.m
- Contents.m
- make_cell
- make_cell
- minimize
- minimize
- mslinearsolve
- mslinearsolve
- msquadsolve
- msquadsolve
- qp_learn
- qp_learn
- quadsolve
- quadsolve
- rsptrain
- rsptrain
- rsptrain
- rsptrain
- rsptrain
- rsptrain
- rsptrainmodsel
- rsptrainmodsel
- rsp_max
- rsp_max
- slinearsolve
- slinearsolve
- squadsolve
- squadsolve
- svm_multi_init
- svm_multi_init
- svm_multi_pred
- svm_multi_pred
- svm_multi_predK
- svm_multi_predK
- svr2w2
- svr2w2
CanlabCore/External/spider/Optimization/leon_src
CanlabCore/External/spider/Optimization/libsvm
CanlabCore/External/spider/Optimization/libsvm_classifier_spider
CanlabCore/External/spider/Optimization/libsvm_one_class_spider
CanlabCore/External/spider/Optimization/libsvm_regressor_spider
CanlabCore/External/spider/basic/@algorithm
- algorithm
- algorithm
- am_i_data
- am_i_data
- display
- display
- display_simple
- display_simple
- extract
- extract
- gen
- gen
- get_name
- get_name
- isdeferred
- isdeferred
- subsasgn
- subsasgn
- subsref
- subsref
- test
- test
- train
- train
- traintest
- traintest
- traintests
- traintests
CanlabCore/External/spider/basic/@chain
CanlabCore/External/spider/basic/@cv
- cv
- cv
- display
- display
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@data
- concatenate
- concatenate
- data
- data
- display
- display
- get
- get
- get_dim
- get_dim
- get_index
- get_index
- get_name
- get_name
- get_x
- get_x
- get_xy
- get_xy
- get_y
- get_y
- isdeferred
- isdeferred
- partition
- partition
- plot
- plot
- readfrom
- readfrom
- set_name
- set_name
- set_x
- set_x
- set_y
- set_y
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@data_global
- concatenate
- concatenate
- data_global
- data_global
- display
- display
- get
- get
- get_dim
- get_dim
- get_index
- get_index
- get_name
- get_name
- get_x
- get_x
- get_xy
- get_xy
- get_y
- get_y
- isdeferred
- isdeferred
- ismyX
- ismyX
- make_cell
- make_cell
- partition
- partition
- set_name
- set_name
- set_x
- set_x
- set_y
- set_y
- subsasgn
- subsasgn
- subsref
- subsref
CanlabCore/External/spider/basic/@distance
- calc
- calc
- calc
- calc
- chisquared
- chisquared
- distance
- distance
- eq
- eq
- euclid
- euclid
- get_name
- get_name
- get_norm
- get_norm
- linear
- linear
- norm
- norm
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
- YOUR_DISTANCE
- YOUR_DISTANCE
CanlabCore/External/spider/basic/@get_mean
- calc
- calc
- get_mean
- get_mean
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@group
- add
- add
- ctranspose
- ctranspose
- display
- display
- get_name
- get_name
- group
- group
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@kernel
- anisotropic_rbf
- anisotropic_rbf
- calc
- calc
- edit_distance
- edit_distance
- empirical_levenstein
- empirical_levenstein
- emp_feat_map
- emp_feat_map
- emp_feat_map_segments
- emp_feat_map_segments
- eq
- eq
- from_data
- from_data
- gaussian
- gaussian
- get_kernel
- get_kernel
- get_name
- get_name
- get_norm
- get_norm
- kernel
- kernel
- kmgraph
- kmgraph
- kmgraph_classical
- kmgraph_classical
- kondor
- kondor
- kpa
- kpa
- levenstein
- levenstein
- linear
- linear
- linear
- linear
- matching
- matching
- poly
- poly
- poly
- poly
- poly
- poly
- poly_of_ker
- poly_of_ker
- rbf
- rbf
- rbf
- rbf
- rbf_of_dist
- rbf_of_dist
- spikernel
- spikernel
- squared_levenstein
- squared_levenstein
- squared_levenstein
- squared_levenstein
- string_subsequence
- string_subsequence
- subsasgn
- subsasgn
- subsref
- subsref
- symbol_string
- symbol_string
- testing
- testing
- tpoly
- tpoly
- training
- training
- triangular
- triangular
- weighted_linear
- weighted_linear
- weighted_poly
- weighted_poly
- YOUR_KERNEL
- YOUR_KERNEL
CanlabCore/External/spider/basic/@loss
- align
- align
- alignment
- alignment
- AUC
- AUC
- balanced_loss
- balanced_loss
- BER
- BER
- calc
- calc
- class_loss
- class_loss
- confusion_matrix
- confusion_matrix
- epsilon_loss
- epsilon_loss
- get_name
- get_name
- index_loss
- index_loss
- kernel_loss
- kernel_loss
- linear_loss
- linear_loss
- log_loss
- log_loss
- loss
- loss
- N_class_loss
- N_class_loss
- one_class_loss
- one_class_loss
- quadratic_loss
- quadratic_loss
- rmse
- rmse
- roc
- roc
- roc50
- roc50
- sensitivity
- sensitivity
- specificity
- specificity
- squared_corr
- squared_corr
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
- triang_loss
- triang_loss
- weighted_class_loss
- weighted_class_loss
CanlabCore/External/spider/basic/@map
CanlabCore/External/spider/basic/@normalize
- get_name
- get_name
- normalize
- normalize
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@param
- display
- display
- get_name
- get_name
- num2choice
- num2choice
- param
- param
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@spiral
- generate
- generate
- get_name
- get_name
- spiral
- spiral
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/basic/@toy
- generate
- generate
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- toy
- toy
- training
- training
CanlabCore/External/spider/basic/@toy2d
- generate
- generate
- get_name
- get_name
- make_data
- make_data
- rectsample
- rectsample
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- toy2d
- toy2d
- training
- training
CanlabCore/External/spider/basic/@toyreg
- generate
- generate
- get_name
- get_name
- rectsample
- rectsample
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- toyreg
- toyreg
- training
- training
CanlabCore/External/spider/clust/@kmeans
- distortion
- distortion
- get_name
- get_name
- kmeans
- kmeans
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/clust/@kpca
CanlabCore/External/spider/clust/@kvq
- circplot
- circplot
- get_name
- get_name
- kvq
- kvq
- optimize
- optimize
- plot
- plot
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/clust/@one_class_svm
- data_square_plot
- data_square_plot
- get_name
- get_name
- get_w.m
- get_w.m
- one_class_svm.m
- one_class_svm.m
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/density/@bayes
- bayes
- bayes
- generate
- generate
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/density/@gauss
- gauss
- gauss
- generate
- generate
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/density/@parzen
- data_square_plot
- data_square_plot
- get_name
- get_name
- parzen
- parzen
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/feat_sel/@rfe
- get_name
- get_name
- plot
- plot
- rfe
- rfe
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/functions
- alignk
- alignk
- analysis.m
- analysis.m
- calc_corrt_test
- calc_corrt_test
- calc_group
- calc_group
- calc_mean
- calc_mean
- calc_mean_fast
- calc_mean_fast
- calc_wilcoxon
- calc_wilcoxon
- convert_mc
- convert_mc
- correst
- correst
- cv_mean
- cv_mean
- equal
- equal
- errorbar2
- errorbar2
- eval_hyper.m
- eval_hyper.m
- eval_name.m
- eval_name.m
- Fspikernel
- Fspikernel
- Ftrunc
- Ftrunc
- genCode
- genCode
- get_methods
- get_methods
- gpS00
- gpS00
- group2cell
- group2cell
- group2vec
- group2vec
- incremental_invert
- incremental_invert
- libsvm_save
- libsvm_save
- make_html_contents
- make_html_contents
- make_html_help
- make_html_help
- minimize
- minimize
- muteinf
- muteinf
- myexist
- myexist
- names
- names
- plotranking
- plotranking
- plots
- plots
- readranking
- readranking
- wekaArgumentString
- wekaArgumentString
- wekaCategoricalData
- wekaCategoricalData
- wekaGetFeaturesFromGraph
- wekaGetFeaturesFromGraph
- wekaInstalled
- wekaInstalled
- wekaNumericalData
- wekaNumericalData
CanlabCore/External/spider/mclass/@one_vs_one
- display
- display
- get_name
- get_name
- get_w
- get_w
- get_w2
- get_w2
- one_vs_one
- one_vs_one
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/mclass/@one_vs_rest
- display
- display
- get_name
- get_name
- get_w
- get_w
- get_w2
- get_w2
- one_vs_rest
- one_vs_rest
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/mod_sel/@bayessel
- bayessel
- bayessel
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/mod_sel/@gridsel
- get_name
- get_name
- gridsel
- gridsel
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/pat/@adaboost
- adaboost
- adaboost
- get_name
- get_name
- get_w
- get_w
- plot
- plot
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/pat/@bagging
- bagging
- bagging
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/pat/@knn
- dist
- dist
- get_name
- get_name
- globals.m
- globals.m
- knn
- knn
- plot
- plot
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- test_slow
- test_slow
- training
- training
CanlabCore/External/spider/pat/@platt
CanlabCore/External/spider/pat/@svm
- add_ridge
- add_ridge
- get_name
- get_name
- get_w
- get_w
- plot.m
- plot.m
- subsasgn
- subsasgn
- subsref
- subsref
- svm
- svm
- testing
- testing
- training
- training
CanlabCore/External/spider/pat/@template
- get_name
- get_name
- subsasgn
- subsasgn
- subsref
- subsref
- template
- template
- testing
- testing
- training
- training
CanlabCore/External/spider/redset/@rss_mp
- finvupdate.m
- finvupdate.m
- get_name
- get_name
- rss_mp.m
- rss_mp.m
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training.m
- training.m
CanlabCore/External/spider/reg/@gproc
- get_name
- get_name
- get_w
- get_w
- gproc
- gproc
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/reg/@multi_reg
- display
- display
- get_name
- get_name
- get_w
- get_w
- multi_reg
- multi_reg
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/reg/@multi_rr
- get_name
- get_name
- get_w
- get_w
- loo
- loo
- multi_rr.m
- multi_rr.m
- subsasgn
- subsasgn
- subsref
- subsref
- testing
- testing
- training
- training
CanlabCore/External/spider/reg/@svr
- get_name
- get_name
- get_w
- get_w
- subsasgn
- subsasgn
- subsref
- subsref
- svr
- svr
- testing
- testing
- training
- training
CanlabCore/External/umap/umap
- canlab_umap_example_iris_dataset.m
- canlab_umap_example_iris_dataset.m
- categorical_simplicial_set_intersection
- categorical_simplicial_set_intersection
- CheckUmapFolder
- CheckUmapFolder
- choose_optimize_layout
- choose_optimize_layout
- clip
- clip
- Coder
- Coder
- CommaFormat
- CommaFormat
- compute_membership_strengths
- compute_membership_strengths
- cross_entropy
- cross_entropy
- debugTiming
- debugTiming
- detectUnsupervised
- detectUnsupervised
- divide_sparse
- divide_sparse
- fast_intersection
- fast_intersection
- find_ab_params
- find_ab_params
- fuzzy_simplicial_set
- fuzzy_simplicial_set
- general_simplicial_set_intersection
- general_simplicial_set_intersection
- general_sset_intersection
- general_sset_intersection
- generate_synthetic_set
- generate_synthetic_set
- initJava
- initJava
- init_transform
- init_transform
- InstallMexAndExe
- InstallMexAndExe
- KnnFind
- KnnFind
- ln_freq_var
- ln_freq_var
- lobpcg.m
- lobpcg.m
- make_epochs_per_sample
- make_epochs_per_sample
- nearest_neighbors
- nearest_neighbors
- neg_sampling_objective
- neg_sampling_objective
- NnDescent
- NnDescent
- optimize_layout
- optimize_layout
- optimize_layout2
- optimize_layout2
- optimize_layout3
- optimize_layout3
- optimize_layout4
- optimize_layout4
- optimize_layout5
- optimize_layout5
- parseArguments
- parseArguments
- pdist_plot
- pdist_plot
- perturb_classes
- perturb_classes
- plot_objectives
- plot_objectives
- prec_rec_plot
- prec_rec_plot
- probability_bin.m
- probability_bin.m
- probability_bin_labels
- probability_bin_labels
- probability_means_weights_ptrs
- probability_means_weights_ptrs
- remove_sparse
- remove_sparse
- reset_local_connectivity
- reset_local_connectivity
- resupervise
- resupervise
- run_examples
- run_examples
- run_umap
- run_umap
- smooth_knn_dist
- smooth_knn_dist
- spectral_layout
- spectral_layout
- spectral_layout_binned
- spectral_layout_binned
- StochasticGradientDescent
- StochasticGradientDescent
- Supervisors
- Supervisors
- Template
- Template
- TestDistFunc
- TestDistFunc
- Test_Mahal
- Test_Mahal
- test_minkowski
- test_minkowski
- trainOptimize
- trainOptimize
- trans2_optimize_layout
- trans2_optimize_layout
- UMAP
- UMAP
- UmapExamples
- UmapExamples
- UmapPython
- UmapPython
- UmapUtil
- UmapUtil
- UMAP_extra_results
- UMAP_extra_results
- UstTest
- UstTest
CanlabCore/External/umap/util
- AdaptiveBins
- AdaptiveBins
- ask
- ask
- askYesOrNo
- askYesOrNo
- BasicMap
- BasicMap
- Branch
- Branch
- bsearch
- bsearch
- CellBasics
- CellBasics
- clockwise
- clockwise
- close
- close
- ClusterPlots
- ClusterPlots
- Clusters
- Clusters
- ColorsByName
- ColorsByName
- decodeMsg.m
- decodeMsg.m
- Density
- Density
- DensityBiased
- DensityBiased
- FalsePositiveNegative
- FalsePositiveNegative
- File
- File
- FileBasics
- FileBasics
- findjobj
- findjobj
- findjobj_fast
- findjobj_fast
- fixClusterTear
- fixClusterTear
- FMeasureMerger
- FMeasureMerger
- getjframe
- getjframe
- getMessageType
- getMessageType
- getMsgTypeAndOptions.m
- getMsgTypeAndOptions.m
- gridEdge
- gridEdge
- Gui
- Gui
- Html
- Html
- inputDlg
- inputDlg
- javaPointToMatLab
- javaPointToMatLab
- JavaProperties
- JavaProperties
- javaScreens
- javaScreens
- LabelBasics
- LabelBasics
- Map
- Map
- MatBasics
- MatBasics
- msg
- msg
- msgBox
- msgBox
- msgError
- msgError
- msgModalOnTop
- msgModalOnTop
- msgWarning
- msgWarning
- MultiProps
- MultiProps
- noTip
- noTip
- Plots
- Plots
- PopUp
- PopUp
- ProbabilityDensity2
- ProbabilityDensity2
- QfHiDM
- QfHiDM
- QfTable
- QfTable
- QfTree
- QfTree
- Radio
- Radio
- reportClusterMerging
- reportClusterMerging
- resizeJavaPrefs
- resizeJavaPrefs
- run_HiD_match
- run_HiD_match
- run_QfTree
- run_QfTree
- setAlwaysOnTopTimer
- setAlwaysOnTopTimer
- showMsg
- showMsg
- SortGui
- SortGui
- sortStructs
- sortStructs
- SortTable
- SortTable
- String
- String
- StringArray
- StringArray
- TableBasics
- TableBasics
- ToolBar
- ToolBar
- ToolBarMethods
- ToolBarMethods
- TopItems
- TopItems
- TreeMapOfMany
- TreeMapOfMany
- WebDownload
- WebDownload
CanlabCore/Filename_tools
- canlab_get_underlay_image
- canlab_get_underlay_image
- canlab_list_files
- canlab_list_files
- canlab_list_subjects
- canlab_list_subjects
- check_valid_imagename
- check_valid_imagename
- copy_image_files
- copy_image_files
- delete_ana_imgs
- delete_ana_imgs
- dicom_tarzip
- dicom_tarzip
- escapeForShell
- escapeForShell
- expand_4d_filenames
- expand_4d_filenames
- extract_bids_info
- extract_bids_info
- filenames
- filenames
- filename_get_new_root_dir
- filename_get_new_root_dir
- files_to_bids_tbl
- files_to_bids_tbl
- getfullpath
- getfullpath
- gunzip_image_names_if_gz
- gunzip_image_names_if_gz
- importdata2table
- importdata2table
- nums_from_text
- nums_from_text
- read_excel
- read_excel
- remove_disdaq_vols
- remove_disdaq_vols
- rename_lowercase
- rename_lowercase
- rename_uppercase
- rename_uppercase
- scan_get_files
- scan_get_files
- scn_get_image_names
- scn_get_image_names
- sort_image_filenames
- sort_image_filenames
CanlabCore/GLM_Batch_tools
- canlab_glm_convolve
- canlab_glm_convolve
- canlab_glm_getinfo
- canlab_glm_getinfo
- canlab_glm_group_levels
- canlab_glm_group_levels
- canlab_glm_group_levels_run1input
- canlab_glm_group_levels_run1input
- canlab_glm_maskstats
- canlab_glm_maskstats
- canlab_glm_publish
- canlab_glm_publish
- canlab_glm_publish_group_levels.m
- canlab_glm_publish_group_levels.m
- canlab_glm_publish_subject_levels.m
- canlab_glm_publish_subject_levels.m
- canlab_glm_roistats
- canlab_glm_roistats
- canlab_glm_subject_levels
- canlab_glm_subject_levels
- canlab_glm_subject_levels_old
- canlab_glm_subject_levels_old
- canlab_glm_subject_levels_run1subject
- canlab_glm_subject_levels_run1subject
- canlab_glm_subject_levels_run1subject_old
- canlab_glm_subject_levels_run1subject_old
- canlab_prep_bidsdir
- canlab_prep_bidsdir
- canlab_spm_glm_extract_trial_info_and_betas
- canlab_spm_glm_extract_trial_info_and_betas
- promptDSGN
- promptDSGN
CanlabCore/GLM_Batch_tools/CANLab_spm_toolbox
CanlabCore/GLM_Batch_tools/extra
CanlabCore/HRF_Est_Toolbox2
- Anneal_Logit
- Anneal_Logit
- Det_Logit
- Det_Logit
- Example.m
- Example.m
- Example2.m
- Example2.m
- Fit_Canonical_HRF
- Fit_Canonical_HRF
- Fit_Logit2
- Fit_Logit2
- Fit_NLgamma
- Fit_NLgamma
- Fit_sFIR
- Fit_sFIR
- Fit_sFIR_epochmodulation
- Fit_sFIR_epochmodulation
- Fit_Spline
- Fit_Spline
- Get_Logit
- Get_Logit
- get_parameters2
- get_parameters2
- HMHRFest
- HMHRFest
- hrf_fit_one_voxel
- hrf_fit_one_voxel
- ilogit
- ilogit
- PowerLoss
- PowerLoss
- PowerSim.m
- PowerSim.m
- ResidScan
- ResidScan
- sFIR_estimation
- sFIR_estimation
CanlabCore/HRF_Est_Toolbox2/EstHRF_inAtlas
- animate
- animate
- describeHRF
- describeHRF
- detectPeaksTroughs
- detectPeaksTroughs
- EstimateHRF_inAtlas
- EstimateHRF_inAtlas
- extractHRF
- extractHRF
- fitHRF_batch
- fitHRF_batch
- generateConditionTS
- generateConditionTS
- generateHRFTable
- generateHRFTable
- HRF_avg
- HRF_avg
- hrf_fit
- hrf_fit
- makeHRFstruct
- makeHRFstruct
- plotHRF
- plotHRF
- plotRegionalHrfSummaries
- plotRegionalHrfSummaries
- process_HRF_dir
- process_HRF_dir
CanlabCore/HRF_Est_Toolbox2/New_fminsearchbnd
CanlabCore/HRF_Est_Toolbox2/Old_stuff
- Anneal_Logit_allstim
- Anneal_Logit_allstim
- cost
- cost
- cost2
- cost2
- cost_allstim
- cost_allstim
- cost_allstim_2
- cost_allstim_2
- cost_allstim_2
- cost_allstim_2
- Det_Logit
- Det_Logit
- dilogit_dt2
- dilogit_dt2
- Fit_Logit_allstim
- Fit_Logit_allstim
- Fit_Logit_allstim_2
- Fit_Logit_allstim_2
- Fit_sFIR
- Fit_sFIR
- get_parameters_logit
- get_parameters_logit
- Get_parameters_Logit2_2hrfs
- Get_parameters_Logit2_2hrfs
- ScanSim4.m
- ScanSim4.m
CanlabCore/HRF_Est_Toolbox2/Old_stuff/More_recent_old_stuff
- Anneal_Logit
- Anneal_Logit
- Det_Logit
- Det_Logit
- Example.m
- Example.m
- Example2.m
- Example2.m
- Example_old.m
- Example_old.m
- Fit_Canonical_HRF
- Fit_Canonical_HRF
- Fit_Logit
- Fit_Logit
- Fit_Logit_allstim
- Fit_Logit_allstim
- Fit_Logit_allstim_2
- Fit_Logit_allstim_2
- Fit_sFIR
- Fit_sFIR
- get_logit
- get_logit
- get_logit_2
- get_logit_2
- get_parameters2
- get_parameters2
- ilogit
- ilogit
- PowerLoss
- PowerLoss
- PowerSim.m
- PowerSim.m
- ResidScan
- ResidScan
- ScanSim4.m
- ScanSim4.m
CanlabCore/Image_computation_tools
- apply_derivative_boost
- apply_derivative_boost
- canlab_create_wm_ventricle_masks
- canlab_create_wm_ventricle_masks
- fisherp
- fisherp
- get_mask_vol
- get_mask_vol
- image_eval_function
- image_eval_function
- image_eval_function_multisubj
- image_eval_function_multisubj
- image_histogram1d
- image_histogram1d
- maskImg.m
- maskImg.m
- mask_create_from_image_set
- mask_create_from_image_set
- mask_create_results_mask
- mask_create_results_mask
- mask_fisher
- mask_fisher
- mask_image
- mask_image
- mask_intersection
- mask_intersection
- mask_intersection2
- mask_intersection2
- mask_stouffer
- mask_stouffer
- mask_union
- mask_union
- mean_image
- mean_image
- my_function_name
- my_function_name
- percent_sig_image
- percent_sig_image
- reslice_imgs
- reslice_imgs
- reverse_mask
- reverse_mask
- scn_num_volumes
- scn_num_volumes
- scn_write_plane
- scn_write_plane
- spm_htw_from_fit
- spm_htw_from_fit
- tor_global
- tor_global
- tor_spm_mean_ui
- tor_spm_mean_ui
CanlabCore/Image_space_tools
- check_spm_mat
- check_spm_mat
- check_spm_matfiles
- check_spm_matfiles
- img2voxel
- img2voxel
- mask2voxel
- mask2voxel
- mm2voxel.m
- mm2voxel.m
- mni2tal
- mni2tal
- scn_map_image
- scn_map_image
- scn_resample_voxel_size
- scn_resample_voxel_size
- tal2mni
- tal2mni
- tal2vox
- tal2vox
- transform_coordinates
- transform_coordinates
- voxel2mask
- voxel2mask
- voxel2mm
- voxel2mm
CanlabCore/Image_thresholding
- clusterSizeMask
- clusterSizeMask
- cl_ext_3dClustSim
- cl_ext_3dClustSim
- cl_ext_make_resid
- cl_ext_make_resid
- cl_ext_spm_grf
- cl_ext_spm_grf
- cl_ext_spm_spm
- cl_ext_spm_spm
- FDR
- FDR
- threshold_imgs
- threshold_imgs
CanlabCore/Index_image_manip_tools
- flip_endianness
- flip_endianness
- iimg_check_indx
- iimg_check_indx
- iimg_check_volinfo
- iimg_check_volinfo
- iimg_clusters2indx
- iimg_clusters2indx
- iimg_cluster_extent
- iimg_cluster_extent
- iimg_cluster_index
- iimg_cluster_index
- iimg_cluster_intersect
- iimg_cluster_intersect
- iimg_cluster_prune
- iimg_cluster_prune
- iimg_get_data
- iimg_get_data
- iimg_indx2clusters
- iimg_indx2clusters
- iimg_indx2contiguousxyz
- iimg_indx2contiguousxyz
- iimg_intersection
- iimg_intersection
- iimg_make_sure_indx
- iimg_make_sure_indx
- iimg_mask
- iimg_mask
- iimg_multi_threshold
- iimg_multi_threshold
- iimg_princomp
- iimg_princomp
- iimg_princomp_display
- iimg_princomp_display
- iimg_read_img
- iimg_read_img
- iimg_read_vols
- iimg_read_vols
- iimg_reconstruct_3dvol
- iimg_reconstruct_3dvol
- iimg_reconstruct_vols
- iimg_reconstruct_vols
- iimg_reslice
- iimg_reslice
- iimg_smooth_3d
- iimg_smooth_3d
- iimg_sphere_timeseries
- iimg_sphere_timeseries
- iimg_stouffer
- iimg_stouffer
- iimg_threshold
- iimg_threshold
- iimg_weighted_ttest
- iimg_weighted_ttest
- iimg_write_images
- iimg_write_images
- iimg_xyz2indx
- iimg_xyz2indx
- iimg_xyz2spheres
- iimg_xyz2spheres
- nans2zeros
- nans2zeros
CanlabCore/Misc_utilities
- blank_struct
- blank_struct
- canlab_mat2cell
- canlab_mat2cell
- canlab_print_legend_text
- canlab_print_legend_text
- cellregexp
- cellregexp
- CERTreader
- CERTreader
- checkMatlabVersion
- checkMatlabVersion
- check_matlab_version
- check_matlab_version
- circle
- circle
- combine_structs
- combine_structs
- condf2indic
- condf2indic
- depfun_aggregate
- depfun_aggregate
- distance
- distance
- distance_euclid
- distance_euclid
- documentation_template.m
- documentation_template.m
- erase_and_display
- erase_and_display
- erase_string
- erase_string
- estimate_time_to_complete
- estimate_time_to_complete
- explode
- explode
- fast_conv_fft
- fast_conv_fft
- format_text_letters_only
- format_text_letters_only
- getRandom
- getRandom
- get_first_help_lines
- get_first_help_lines
- implode
- implode
- indic2condf
- indic2condf
- naninsert
- naninsert
- nanremove
- nanremove
- oneinsert
- oneinsert
- orthviews_multiple_objs
- orthviews_multiple_objs
- pad
- pad
- padwithnan
- padwithnan
- parse_char_to_cell
- parse_char_to_cell
- parse_edat_txt
- parse_edat_txt
- print_matrix
- print_matrix
- progressbar
- progressbar
- publish_obj_oriented_help
- publish_obj_oriented_help
- read_edat_output_2008
- read_edat_output_2008
- remove_str_from_cell
- remove_str_from_cell
- robustcsvread
- robustcsvread
- scn_get_datetime
- scn_get_datetime
- scn_mat_conform
- scn_mat_conform
- search_struct_fields
- search_struct_fields
- sec2hms
- sec2hms
- setFigHeight
- setFigHeight
- setFigWidth
- setFigWidth
- spmify
- spmify
- spm_defaults
- spm_defaults
- string2indicator
- string2indicator
- string_boolean_select
- string_boolean_select
- strip_git_dirs
- strip_git_dirs
- strip_path_dirs
- strip_path_dirs
- strip_svn_dirs
- strip_svn_dirs
- strrep_recurse
- strrep_recurse
- struct_strrep
- struct_strrep
- subplots
- subplots
- table_extract_data_by_subject
- table_extract_data_by_subject
- tor_ga
- tor_ga
- zeroinsert
- zeroinsert
CanlabCore/Model_building_tools
- canlab_spm_first_level_spec.m
- canlab_spm_first_level_spec.m
- comp_model.m
- comp_model.m
- create_block_design
- create_block_design
- create_design_single_event
- create_design_single_event
- create_random_er_design
- create_random_er_design
- create_random_onsets
- create_random_onsets
- design_matrix.m
- design_matrix.m
- fmri_spline_basis
- fmri_spline_basis
- getPredictors
- getPredictors
- hrf_saturation
- hrf_saturation
- ideal_deconv6
- ideal_deconv6
- intercept_model
- intercept_model
- make_ideal_data
- make_ideal_data
- modifiedconv
- modifiedconv
- modifiedconv_wager2005
- modifiedconv_wager2005
- onsets2delta
- onsets2delta
- onsets2dx
- onsets2dx
- onsets2fmridesign
- onsets2fmridesign
- onsets2parametric_mod_X
- onsets2parametric_mod_X
- plot_ideal_deconv5
- plot_ideal_deconv5
- spm_mat2batchinput
- spm_mat2batchinput
- tor_make_deconv_mtx3
- tor_make_deconv_mtx3
CanlabCore/OptimizeDesign11
CanlabCore/OptimizeDesign11/GA2
- calcEfficiency
- calcEfficiency
- cond2reg
- cond2reg
- constrain_toverlap
- constrain_toverlap
- construct_model
- construct_model
- construct_model
- construct_model
- ga2
- ga2
- getv
- getv
- model_setup_ui.m
- model_setup_ui.m
- paramvec2onsets
- paramvec2onsets
- tor_make_deconv_mtx
- tor_make_deconv_mtx
- X2onsets
- X2onsets
CanlabCore/OptimizeDesign11/GA3
- canonical_autocorrelation
- canonical_autocorrelation
- downsample_delta
- downsample_delta
- efficiency2
- efficiency2
- example_get_sigma.m
- example_get_sigma.m
- example_script_make_rt_predictor.m
- example_script_make_rt_predictor.m
- example_script_onsets_to_power.m
- example_script_onsets_to_power.m
- example_script_test_beta_variance.m
- example_script_test_beta_variance.m
- ga2power
- ga2power
- ga3power
- ga3power
- ga3power
- ga3power
- genMseq
- genMseq
- hp_filter_plot
- hp_filter_plot
- hrf_power
- hrf_power
- modelSaturation
- modelSaturation
- onsets2efficiency2
- onsets2efficiency2
- power_map1
- power_map1
- psdplot_x_vs_acf.m
- psdplot_x_vs_acf.m
- rt2delta
- rt2delta
- tmp_onsets2dx.m
- tmp_onsets2dx.m
- xpower
- xpower
- xzpower
- xzpower
CanlabCore/OptimizeDesign11/GA3/Sobol
- bit_hi1_base_2
- bit_hi1_base_2
- bit_lo0_base_2
- bit_lo0_base_2
- exor
- exor
- get_seed
- get_seed
- i_random
- i_random
- r_random
- r_random
- sobol
- sobol
- sobol_test.m
- sobol_test.m
- sobol_test01.m
- sobol_test01.m
- sobol_test02.m
- sobol_test02.m
- sobol_test03.m
- sobol_test03.m
- sobol_test04.m
- sobol_test04.m
- sobol_test05.m
- sobol_test05.m
- timestamp.m
- timestamp.m
- uniform
- uniform
CanlabCore/OptimizeDesign11/GA3/georges_tourtellot
CanlabCore/OptimizeDesign11/M-sequence
CanlabCore/OptimizeDesign11/M-sequence/mseq
- autocorrFnct
- autocorrFnct
- balancedRnd
- balancedRnd
- bin2m
- bin2m
- Contents.m
- Contents.m
- cycorr
- cycorr
- efficiencyOFexpDesigns2.m
- efficiencyOFexpDesigns2.m
- efficiencyOFexpDesignsCorrMtrx.m
- efficiencyOFexpDesignsCorrMtrx.m
- effOFexpDesignsNoOverlap2.m
- effOFexpDesignsNoOverlap2.m
- effOFexpDesignsNoOverlap3.m
- effOFexpDesignsNoOverlap3.m
- effOFexpDesignsNoOverlap7.m
- effOFexpDesignsNoOverlap7.m
- m2bin
- m2bin
- makeEventMtrx
- makeEventMtrx
- mseq
- mseq
CanlabCore/OptimizeDesign11/core_functions
- breedorgs
- breedorgs
- calcEfficiency
- calcEfficiency
- calcFreqDev
- calcFreqDev
- counterbalance.m
- counterbalance.m
- designvector2model
- designvector2model
- dna2model
- dna2model
- dna2model_epochs
- dna2model_epochs
- dna2model_epochs
- dna2model_epochs
- dna2rna
- dna2rna
- efficency
- efficency
- efficency
- efficency
- ga_model2onsets
- ga_model2onsets
- getCounterBal
- getCounterBal
- getFitnessRank
- getFitnessRank
- getHPfilter
- getHPfilter
- getK
- getK
- getMaxInARow
- getMaxInARow
- getOverallFitness
- getOverallFitness
- getPredictors
- getPredictors
- getRandfxPredictors
- getRandfxPredictors
- getSmoothing
- getSmoothing
- getv
- getv
- getvif
- getvif
- hoxsetup
- hoxsetup
- insert_rests
- insert_rests
- modelDiagnostics2
- modelDiagnostics2
- onsets2efficiency
- onsets2efficiency
- resample_gnu.m
- resample_gnu.m
- rna2model
- rna2model
- sampleInSeconds
- sampleInSeconds
- tenPercentRandom
- tenPercentRandom
- tor_make_deconv_mtx2
- tor_make_deconv_mtx2
- transform2block
- transform2block
- transform2switches
- transform2switches
CanlabCore/OptimizeDesign11/example_scripts
- ga_eli.m
- ga_eli.m
- ga_example_script.m
- ga_example_script.m
- ga_example_script_5types.m
- ga_example_script_5types.m
- ga_example_script_6types_cbal.m
- ga_example_script_6types_cbal.m
- ga_example_script_basic.m
- ga_example_script_basic.m
- ga_example_script_factorial.m
- ga_example_script_factorial.m
- ga_example_script_jitter.m
- ga_example_script_jitter.m
- ga_example_script_mixed_blk_er.m
- ga_example_script_mixed_blk_er.m
- ga_foo.m
- ga_foo.m
- ga_text_script_epochs.m
- ga_text_script_epochs.m
- ga_text_script_hox.m
- ga_text_script_hox.m
- randsearch_text_script.m
- randsearch_text_script.m
CanlabCore/OptimizeDesign11/exhaustive_mapping
- param_map
- param_map
- rundesignsim.m
- rundesignsim.m
- rundesignsimISI.m
- rundesignsimISI.m
- rundesignsimMAP.m
- rundesignsimMAP.m
- rundesignsimMAP2.m
- rundesignsimMAP2.m
- rundesignsimMAP2_placebo.m
- rundesignsimMAP2_placebo.m
CanlabCore/OptimizeDesign11/faceGA
CanlabCore/OptimizeDesign11/other_functions
- breedorgs2
- breedorgs2
- designsim
- designsim
- designsim_gui_script.m
- designsim_gui_script.m
- get_noGA_tdist.m
- get_noGA_tdist.m
- loadM
- loadM
- make1overf
- make1overf
- my_glm
- my_glm
- noisevector
- noisevector
- param_map
- param_map
- plotDelta
- plotDelta
- plotSim
- plotSim
- runsim
- runsim
- summary
- summary
- testlist
- testlist
- testM
- testM
- testM
- testM
- testMvsOther
- testMvsOther
CanlabCore/Parcellation_tools
- cluster_princomp
- cluster_princomp
- inconsistent
- inconsistent
- mask_princomp
- mask_princomp
- parcel_clusters
- parcel_clusters
- parcel_cl_nmds
- parcel_cl_nmds
- parcel_cl_nmds_plots
- parcel_cl_nmds_plots
- parcel_complete_sets
- parcel_complete_sets
- parcel_images
- parcel_images
CanlabCore/ROI_drawing_tools
- add2mask
- add2mask
- clusters2roimask
- clusters2roimask
- draw_anatomical_roi.m
- draw_anatomical_roi.m
- draw_anatomical_roi_2008
- draw_anatomical_roi_2008
- sphere_mask
- sphere_mask
CanlabCore/Statistics_tools
- ancova
- ancova
- arp_V
- arp_V
- barplot_get_within_ste
- barplot_get_within_ste
- bayes_get_probabilities
- bayes_get_probabilities
- bayes_get_probabilities_2010
- bayes_get_probabilities_2010
- bayes_meta_feature_abstract
- bayes_meta_feature_abstract
- BCa
- BCa
- bct_toolbox_undirected_graph_metrics
- bct_toolbox_undirected_graph_metrics
- binotest
- binotest
- binotest_dependent
- binotest_dependent
- Bspline
- Bspline
- cancor
- cancor
- canlab_connectivity_predict
- canlab_connectivity_predict
- canlab_fast_euclidean_distance
- canlab_fast_euclidean_distance
- canlab_pattern_similarity
- canlab_pattern_similarity
- canlab_run_paired_SVM
- canlab_run_paired_SVM
- canlab_variance_decomposition
- canlab_variance_decomposition
- classify_bayes
- classify_bayes
- classify_choose_most_likely
- classify_choose_most_likely
- classify_mds_plot.m
- classify_mds_plot.m
- classify_naive_bayes
- classify_naive_bayes
- classify_naive_bayes_2010
- classify_naive_bayes_2010
- classify_naive_bayes_objfun
- classify_naive_bayes_objfun
- classify_viz_regions
- classify_viz_regions
- cluster_confusion_matrix
- cluster_confusion_matrix
- cohens_d_2sample
- cohens_d_2sample
- ContinuousAccuracy
- ContinuousAccuracy
- contrast_code
- contrast_code
- correlation
- correlation
- correlation_fast_series
- correlation_fast_series
- correlation_to_text
- correlation_to_text
- correl_compare_dep
- correl_compare_dep
- correl_compare_dep_permtest
- correl_compare_dep_permtest
- correl_compare_dep_search
- correl_compare_dep_search
- correl_compare_indep
- correl_compare_indep
- correl_compare_indep_inputr
- correl_compare_indep_inputr
- correl_compare_permute
- correl_compare_permute
- corr_within_between
- corr_within_between
- createFit
- createFit
- create_orthogonal_contrast_set
- create_orthogonal_contrast_set
- dice_coeff_image
- dice_coeff_image
- doquality
- doquality
- effect_size_CI
- effect_size_CI
- exactfrsd
- exactfrsd
- exhaustive_map
- exhaustive_map
- fisherz
- fisherz
- fit_gls
- fit_gls
- fit_gls_brain
- fit_gls_brain
- F_test_full_vs_red
- F_test_full_vs_red
- F_test_no_intercept
- F_test_no_intercept
- getmeanquality
- getmeanquality
- glmfit_general
- glmfit_general
- glmfit_multilevel
- glmfit_multilevel
- glmfit_multilevel_varexplained
- glmfit_multilevel_varexplained
- glm_table
- glm_table
- holm_sidak
- holm_sidak
- ICC
- ICC
- intercept
- intercept
- knn_classify_cv_by_profile
- knn_classify_cv_by_profile
- loess_multilevel
- loess_multilevel
- matrix_direct_effects
- matrix_direct_effects
- matrix_direct_effects_ridge
- matrix_direct_effects_ridge
- matrix_eval_function
- matrix_eval_function
- mediansplit
- mediansplit
- monotonic_regression
- monotonic_regression
- moving_average
- moving_average
- noise_arp
- noise_arp
- nonlin_fit
- nonlin_fit
- nonlin_parammod_predfun
- nonlin_parammod_predfun
- nonlin_param_modulator
- nonlin_param_modulator
- nonlin_param_mod_brain
- nonlin_param_mod_brain
- pairwise_diffs
- pairwise_diffs
- partition_variables_indevel
- partition_variables_indevel
- permute_setupperms
- permute_setupperms
- permute_signtest
- permute_signtest
- plssquash
- plssquash
- power_calc_find_min_effect_size
- power_calc_find_min_effect_size
- princomp_largedata
- princomp_largedata
- prplot_multilevel
- prplot_multilevel
- r2z
- r2z
- RB_empirical_bayes_params
- RB_empirical_bayes_params
- regression_table
- regression_table
- regress_best_subsets_ga
- regress_best_subsets_ga
- repeated_ancova
- repeated_ancova
- resid
- resid
- rmanova2
- rmanova2
- robust_reg_pooled
- robust_reg_pooled
- roc_boot
- roc_boot
- roc_calc
- roc_calc
- roc_plot
- roc_plot
- rsquare_calc
- rsquare_calc
- rsquare_multiple_regions_multilevel
- rsquare_multiple_regions_multilevel
- scale_within_condition
- scale_within_condition
- scn_stats_helper_functions
- scn_stats_helper_functions
- sdt_A
- sdt_A
- searchlight_applymask
- searchlight_applymask
- searchlight_applymask_collate
- searchlight_applymask_collate
- searchlight_correlation
- searchlight_correlation
- searchlight_disti
- searchlight_disti
- searchlight_dream
- searchlight_dream
- searchlight_modcomp
- searchlight_modcomp
- searchlight_predict
- searchlight_predict
- searchlight_saveresults
- searchlight_saveresults
- shift_correl
- shift_correl
- shift_signal
- shift_signal
- signtest_matrix
- signtest_matrix
- ste
- ste
- stepwise_tor
- stepwise_tor
- stouffer
- stouffer
- subset_indicator_matrix
- subset_indicator_matrix
- svm_rfe
- svm_rfe
- table2marginalmeans
- table2marginalmeans
- testclustnew
- testclustnew
- tiedrankorder
- tiedrankorder
- time_varying_estimate
- time_varying_estimate
- tscv
- tscv
- tsquaretest
- tsquaretest
- ttest2_printout
- ttest2_printout
- ttest3d
- ttest3d
- t_test2
- t_test2
- var_prctile
- var_prctile
- weighted_glmfit
- weighted_glmfit
- xcorr_multisubject
- xcorr_multisubject
- xcorr_xy_multisubject
- xcorr_xy_multisubject
CanlabCore/Statistics_tools/Cross_validated_Regression
- xval_bestsubsets_brain
- xval_bestsubsets_brain
- xval_cross_classfy
- xval_cross_classfy
- xval_featureselect_nmdscluster
- xval_featureselect_nmdscluster
- xval_lasso_brain
- xval_lasso_brain
- xval_lasso_brain
- xval_lasso_brain
- xval_lasso_trace
- xval_lasso_trace
- xval_regression_bootstrapweightmap_brainplots
- xval_regression_bootstrapweightmap_brainplots
- xval_regression_multisubject
- xval_regression_multisubject
- xval_regression_multisubject
- xval_regression_multisubject
- xval_regression_multisubject_bootstrapweightmap
- xval_regression_multisubject_bootstrapweightmap
- xval_ridge_brain
- xval_ridge_brain
- xval_select_holdout_set
- xval_select_holdout_set
- xval_select_holdout_set_categoricalcovs
- xval_select_holdout_set_categoricalcovs
- xval_simple_ols_featureselect
- xval_simple_ols_featureselect
- xval_simple_ols_loo
- xval_simple_ols_loo
- xval_simple_ols_loo
- xval_simple_ols_loo
- xval_stratified_holdout_leave_whole_subject_out
- xval_stratified_holdout_leave_whole_subject_out
- xval_SVM
- xval_SVM
- xval_SVR
- xval_SVR
CanlabCore/Statistics_tools/Iterative_Generalized_Least_Squares
- igls
- igls
- igls
- igls
- igls
- igls
- igls
- igls
- igls_brain
- igls_brain
- igls_brain_multilev_wrapper.m
- igls_brain_multilev_wrapper.m
- igls_mediation
- igls_mediation
- igls_multicond
- igls_multicond
- igls_orig
- igls_orig
- igls_plot_slopes
- igls_plot_slopes
- igls_simulation_scripts.m
- igls_simulation_scripts.m
- igls_sim_fpr.m
- igls_sim_fpr.m
- igls_vs_weighted_vs_ols_sim1
- igls_vs_weighted_vs_ols_sim1
CanlabCore/Statistics_tools/Single_trial_analysis
- single_trial_analysis
- single_trial_analysis
- single_trial_analysis_tor
- single_trial_analysis_tor
- single_trial_analysis_trialmodels
- single_trial_analysis_trialmodels
- single_trial_setup_models
- single_trial_setup_models
- single_trial_weights
- single_trial_weights
- trial_level_beta3
- trial_level_beta3
CanlabCore/Statistics_tools/Support_functions
- backprojection
- backprojection
- celldat2matrix
- celldat2matrix
- contrast2d
- contrast2d
- contrast3d
- contrast3d
- convert_to_contour
- convert_to_contour
- correlation_to_text
- correlation_to_text
- distosim
- distosim
- dyadic
- dyadic
- makebinary
- makebinary
- othertriangle
- othertriangle
- pdist
- pdist
- randperm
- randperm
- range
- range
- shuffle
- shuffle
- simtodis
- simtodis
- spm2delta
- spm2delta
- spm2dx
- spm2dx
- squareform
- squareform
- stratified_holdout_set
- stratified_holdout_set
- stress
- stress
- weighted_pdist
- weighted_pdist
- xc_stats
- xc_stats
CanlabCore/Testing_Framework
CanlabCore/Visualization_functions
- 3Davi.m
- 3Davi.m
- active_plus_corr_scatterplot_plugin.m
- active_plus_corr_scatterplot_plugin.m
- addbrain
- addbrain
- add_surface
- add_surface
- applycolormap
- applycolormap
- arrow
- arrow
- barplotter
- barplotter
- barplot_colored
- barplot_colored
- barplot_columns
- barplot_columns
- barplot_columns2
- barplot_columns2
- barplot_columns3
- barplot_columns3
- barplot_grouped
- barplot_grouped
- bar_wani
- bar_wani
- bar_wani_2016
- bar_wani_2016
- brainstem_slices_3d
- brainstem_slices_3d
- brain_movie2.m
- brain_movie2.m
- bucknerlab_colors
- bucknerlab_colors
- canlab_canonical_brain_surface_cutaways
- canlab_canonical_brain_surface_cutaways
- canlab_force_directed_graph
- canlab_force_directed_graph
- canlab_redblue_symmetric_colormap
- canlab_redblue_symmetric_colormap
- canlab_results_fmridisplay
- canlab_results_fmridisplay
- close_non_spm_graphics_figures
- close_non_spm_graphics_figures
- cluster_barplot
- cluster_barplot
- cluster_cutaways
- cluster_cutaways
- cluster_image_shape
- cluster_image_shape
- cluster_image_sphere
- cluster_image_sphere
- cluster_orthviews
- cluster_orthviews
- cluster_orthviews_classes
- cluster_orthviews_classes
- cluster_orthviews_montage
- cluster_orthviews_montage
- cluster_orthviews_overlap
- cluster_orthviews_overlap
- cluster_orthviews_overlap2
- cluster_orthviews_overlap2
- cluster_orthviews_overlap_3colors
- cluster_orthviews_overlap_3colors
- cluster_orthviews_showcenters
- cluster_orthviews_showcenters
- cluster_surf
- cluster_surf
- cluster_surf_batch
- cluster_surf_batch
- cluster_surf_batch2
- cluster_surf_batch2
- cl_line_plots
- cl_line_plots
- cl_overlap
- cl_overlap
- colorcube_colors
- colorcube_colors
- colormap_tor
- colormap_tor
- compare_filtered_t
- compare_filtered_t
- compare_slice
- compare_slice
- conf_region
- conf_region
- cprintf
- cprintf
- create_figure
- create_figure
- custom_colors
- custom_colors
- draw_pie_wedge
- draw_pie_wedge
- errorbar_horizontal
- errorbar_horizontal
- errorbar_width
- errorbar_width
- fill_area_around_points
- fill_area_around_points
- format_strings_for_legend
- format_strings_for_legend
- getVertexColors
- getVertexColors
- getVertexColors
- getVertexColors
- getVertexColors_old_backup.m
- getVertexColors_old_backup.m
- get_cluster_volume
- get_cluster_volume
- get_frame
- get_frame
- glassbrain_avi
- glassbrain_avi
- imageCluster
- imageCluster
- imageCluster_block
- imageCluster_block
- imagePatch
- imagePatch
- image_histogram
- image_histogram
- lineplot_columns
- lineplot_columns
- line_plot_multisubject
- line_plot_multisubject
- make3Davi
- make3Davi
- make3Davi_uncompressed
- make3Davi_uncompressed
- makeIndSubjectSliceAVI.m
- makeIndSubjectSliceAVI.m
- makeIndSubjectSliceAVI2.m
- makeIndSubjectSliceAVI2.m
- makeIndSubjectSliceAVI_uncompressed.m
- makeIndSubjectSliceAVI_uncompressed.m
- makelegend
- makelegend
- make_figure_into_orthviews
- make_figure_into_orthviews
- make_ind_avi_uncompressed.m
- make_ind_avi_uncompressed.m
- map_data_to_colormap
- map_data_to_colormap
- mask2surface
- mask2surface
- mdsfig
- mdsfig
- mdsfig_3d
- mdsfig_3d
- mea_visualise
- mea_visualise
- mni_TSU
- mni_TSU
- montage_clusters
- montage_clusters
- montage_clusters_maxslice
- montage_clusters_maxslice
- montage_clusters_medial
- montage_clusters_medial
- montage_clusters_points
- montage_clusters_points
- montage_clusters_text
- montage_clusters_text
- montage_clusters_text2
- montage_clusters_text2
- montage_image_Worsley
- montage_image_Worsley
- movie_of_slice_timeseries
- movie_of_slice_timeseries
- movie_stillframes
- movie_stillframes
- multi_threshold
- multi_threshold
- multi_threshold2
- multi_threshold2
- mvroi_mdsfig_plot2
- mvroi_mdsfig_plot2
- mvroi_mdsfig_plot_sepstates
- mvroi_mdsfig_plot_sepstates
- mvroi_mdsfig_plugin2
- mvroi_mdsfig_plugin2
- mvroi_plot_firs
- mvroi_plot_firs
- mvroi_residplot_plugin.m
- mvroi_residplot_plugin.m
- nmdsfig
- nmdsfig
- nmdsfig1D
- nmdsfig1D
- nmdsfig_fill
- nmdsfig_fill
- nmdsfig_legend
- nmdsfig_legend
- nonmonotonic_regression_plot
- nonmonotonic_regression_plot
- plot3d
- plot3d
- plotbehav
- plotbehav
- plotclustfir
- plotclustfir
- plotDesign
- plotDesign
- plothead.m
- plothead.m
- plot_correlation
- plot_correlation
- plot_correlation_matrix
- plot_correlation_matrix
- plot_correlation_samefig
- plot_correlation_samefig
- plot_dx_hrfs
- plot_dx_hrfs
- plot_ellipse
- plot_ellipse
- plot_error
- plot_error
- plot_horizontal_line
- plot_horizontal_line
- plot_hrf_model_fit
- plot_hrf_model_fit
- plot_joint_hist_contour
- plot_joint_hist_contour
- plot_matrix_cols
- plot_matrix_cols
- plot_parallel_coords
- plot_parallel_coords
- plot_vertical_line
- plot_vertical_line
- prplot
- prplot
- renderCluster_ui
- renderCluster_ui
- renderCluster_ui2.m
- renderCluster_ui2.m
- renderCluster_ui3.m
- renderCluster_ui3.m
- renderCluster_ui4
- renderCluster_ui4
- render_on_cerebellar_flatmap.m
- render_on_cerebellar_flatmap.m
- riverplot_remove_ribbons
- riverplot_remove_ribbons
- roi_contour_map
- roi_contour_map
- scatter_glm
- scatter_glm
- schloss_colors
- schloss_colors
- scn_export_papersetup
- scn_export_papersetup
- scn_export_spm_window
- scn_export_spm_window
- scn_standard_colors
- scn_standard_colors
- seaborn_colors
- seaborn_colors
- selective_average_interactive_view_init
- selective_average_interactive_view_init
- sepplot
- sepplot
- shepardplot
- shepardplot
- sphere_roi_tool
- sphere_roi_tool
- spm_figure
- spm_figure
- spm_orthviews_change_colormap
- spm_orthviews_change_colormap
- spm_orthviews_hotcool_colormap
- spm_orthviews_hotcool_colormap
- spm_orthviews_name_axis
- spm_orthviews_name_axis
- spm_orthviews_showposition
- spm_orthviews_showposition
- spm_orthviews_white_background
- spm_orthviews_white_background
- spm_ov_black2white
- spm_ov_black2white
- standardMRIhead.m
- standardMRIhead.m
- standardMRIlighting
- standardMRIlighting
- surface_cutaway
- surface_cutaway
- surf_plot_tor
- surf_plot_tor
- talairach_clusters
- talairach_clusters
- talairach_cluster_plugin.m
- talairach_cluster_plugin.m
- temp_save_slices.m
- temp_save_slices.m
- testclust_plot_plugin.m
- testclust_plot_plugin.m
- timeseries_prplot
- timeseries_prplot
- tor_3d
- tor_3d
- tor_3d_head.m
- tor_3d_head.m
- tor_fill_steplot
- tor_fill_steplot
- tor_ihb_GetClusters
- tor_ihb_GetClusters
- tor_ihb_GetClusterSet
- tor_ihb_GetClusterSet
- tor_ihb_TalSpace
- tor_ihb_TalSpace
- tor_ihb_UpdateClusterTalVoxSize
- tor_ihb_UpdateClusterTalVoxSize
- tor_polar_plot
- tor_polar_plot
- tor_wedge_plot
- tor_wedge_plot
- values_to_colors
- values_to_colors
- violinplot
- violinplot
- wani_pie
- wani_pie
- xval_lasso_brain_permutation_histogram
- xval_lasso_brain_permutation_histogram
CanlabCore/Visualization_functions/Support
- bar_centers
- bar_centers
- drawbox
- drawbox
- enlarge_axes
- enlarge_axes
- equalize_axes
- equalize_axes
- fill_around_line
- fill_around_line
- lightFollowView
- lightFollowView
- lighthandles
- lighthandles
- lightRestoreSingle
- lightRestoreSingle
- montage_zoom
- montage_zoom
- movie_rotation
- movie_rotation
- movie_tools
- movie_tools
- plot_onsets
- plot_onsets
- squeeze_axes
- squeeze_axes
- steplot
- steplot
- tor_bar_steplot.m
- tor_bar_steplot.m
- tor_fig
- tor_fig
- tor_line_steplot.m
- tor_line_steplot.m
- tor_plot_avgs
- tor_plot_avgs
CanlabCore/Visualization_functions/riverplot
- riverplot_draw_layer
- riverplot_draw_layer
- riverplot_draw_ribbon
- riverplot_draw_ribbon
- riverplot_example_npsplus_bucknerlab.m
- riverplot_example_npsplus_bucknerlab.m
- riverplot_layer_names
- riverplot_layer_names
- riverplot_line
- riverplot_line
- riverplot_recolor_layer2
- riverplot_recolor_layer2
- riverplot_rect
- riverplot_rect
- riverplot_reorder_matrix
- riverplot_reorder_matrix
- riverplot_ribbon
- riverplot_ribbon
- riverplot_ribbon_matrix
- riverplot_ribbon_matrix
- riverplot_set_ribbon_property
- riverplot_set_ribbon_property
- riverplot_toggle_lines
- riverplot_toggle_lines
CanlabCore/canlab_canonical_brains
CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces
CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/src
- create_colin27_to_surf_nearest_neighbor_projections.m
- create_colin27_to_surf_nearest_neighbor_projections.m
- create_colin27_to_surf_projections.m
- create_colin27_to_surf_projections.m
- create_MNI152NLin2009cAsym_to_surf_nearest_neighbor_projections.m
- create_MNI152NLin2009cAsym_to_surf_nearest_neighbor_projections.m
- create_MNI152NLin2009cAsym_to_surf_projections.m
- create_MNI152NLin2009cAsym_to_surf_projections.m
- create_MNI152NLin6Asym_to_surf_nearest_neighbor_projections.m
- create_MNI152NLin6Asym_to_surf_nearest_neighbor_projections.m
- create_MNI152NLin6Asym_to_surf_projections.m
- create_MNI152NLin6Asym_to_surf_projections.m
- spherical_icosahedral_interpolation
- spherical_icosahedral_interpolation
CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/src/private
- create_canlab_surf_file
- create_canlab_surf_file
- hotcool_split_colormap
- hotcool_split_colormap
- map_to_colors
- map_to_colors
CanlabCore/canlab_canonical_brains/Combined_multiatlas_ROI_masks
- add_new_anat_atlas_script.m
- add_new_anat_atlas_script.m
- atlas_labels_combined_info.m
- atlas_labels_combined_info.m
- atlas_spmanatomy_get_cluster
- atlas_spmanatomy_get_cluster
CanlabCore/canlab_canonical_brains/Cortical_ROI_masks
- insula_ribbon_partial_script.m
- insula_ribbon_partial_script.m
- prep_cortical_masks.m
- prep_cortical_masks.m
CanlabCore/canlab_canonical_brains/Thalamus_brainstem_ROIs_surfaces
- draw_coordinate_based_brainstem_rois_2018.m
- draw_coordinate_based_brainstem_rois_2018.m
- draw_dorsal_raphe_rois_2018.m
- draw_dorsal_raphe_rois_2018.m
- draw_pag_roi_2018.m
- draw_pag_roi_2018.m
- draw_sup_inf_colliculus_roi_2018.m
- draw_sup_inf_colliculus_roi_2018.m
- make_brainstem_2018.m
- make_brainstem_2018.m
CanlabCore/diagnostics
- add_nuisance_to_SPMcfg
- add_nuisance_to_SPMcfg
- batch_efficiency
- batch_efficiency
- batch_t_histograms
- batch_t_histograms
- BiasPowerloss
- BiasPowerloss
- canlab_qc_metrics1
- canlab_qc_metrics1
- check_cluster_data
- check_cluster_data
- compare_subjects
- compare_subjects
- compare_subjects256
- compare_subjects256
- displayme
- displayme
- effect_size_map.m
- effect_size_map.m
- ellipse
- ellipse
- fft_calc
- fft_calc
- fmri_mask_thresh_canlab
- fmri_mask_thresh_canlab
- get_filename
- get_filename
- get_filename2
- get_filename2
- hist2
- hist2
- image_intensity_histograms
- image_intensity_histograms
- img_hist
- img_hist
- img_hist2
- img_hist2
- joint_hist
- joint_hist
- make_conv_mtx
- make_conv_mtx
- multivar_dist
- multivar_dist
- orthogonalize
- orthogonalize
- power_from_variance
- power_from_variance
- power_loss
- power_loss
- publish_scn_session_spike_id
- publish_scn_session_spike_id
- qchist
- qchist
- reset_SPMcfg
- reset_SPMcfg
- ResidScan
- ResidScan
- reslice_seg_anatomy
- reslice_seg_anatomy
- saccade_fix_nuisance.m
- saccade_fix_nuisance.m
- sanity_check_fMRI_timemod
- sanity_check_fMRI_timemod
- scale_imgs_by_csf
- scale_imgs_by_csf
- ScanSim4.m
- ScanSim4.m
- scnlab_norm_check
- scnlab_norm_check
- scnlab_norm_check3
- scnlab_norm_check3
- scnlab_pca_check1
- scnlab_pca_check1
- scnlab_pca_denoise_session
- scnlab_pca_denoise_session
- scn_check_vmpfc_signal
- scn_check_vmpfc_signal
- scn_component_rsquare
- scn_component_rsquare
- scn_session_spike_id
- scn_session_spike_id
- scn_spm_choose_hpfilter
- scn_spm_choose_hpfilter
- scn_spm_design_check
- scn_spm_design_check
- scn_spm_get_events_of_interest
- scn_spm_get_events_of_interest
- spm_general_hist
- spm_general_hist
- spm_rfx_hist
- spm_rfx_hist
- struct2yaml
- struct2yaml
- tor_get_physio
- tor_get_physio
- view_betas
- view_betas
CanlabCore/diagnostics/Mis_modeling
CanlabCore/fmridisplay_helper_functions
- clusters2mask2011
- clusters2mask2011
- define_sampling_space
- define_sampling_space
- display_slice
- display_slice
- lighten_underlay_edges
- lighten_underlay_edges
- map_to_world_space
- map_to_world_space
- removepoints
- removepoints
- render_blobs
- render_blobs
- resample_space
- resample_space
CanlabCore/hewma_utility
- change_point
- change_point
- cluster_kmeans_parcel
- cluster_kmeans_parcel
- cnt_runs
- cnt_runs
- ewma5
- ewma5
- Gaussian_mix
- Gaussian_mix
- get_ax_slice
- get_ax_slice
- get_correlationmat
- get_correlationmat
- get_max_t
- get_max_t
- hewma.m
- hewma.m
- hewma2
- hewma2
- hewma2_plot
- hewma2_plot
- hewma_cluster_plot
- hewma_cluster_plot
- hewma_extract_voxel
- hewma_extract_voxel
- hewma_from_raw_timeseries
- hewma_from_raw_timeseries
- hewma_gui
- hewma_gui
- hewma_plot_bivariate
- hewma_plot_bivariate
- hewma_plot_coord_btnupfcn
- hewma_plot_coord_btnupfcn
- hewma_plot_cpmap
- hewma_plot_cpmap
- hewma_plot_runlen
- hewma_plot_runlen
- hewma_save_timeseries
- hewma_save_timeseries
- hewma_timeseries_plot.m
- hewma_timeseries_plot.m
- linear_detrending
- linear_detrending
- timeseries_btwngroups_plot
- timeseries_btwngroups_plot
- timeseries_mc_pvalue
- timeseries_mc_pvalue
- wb_hewma_shell
- wb_hewma_shell
- weighted_reg
- weighted_reg
- weighted_reg_old2
- weighted_reg_old2
- weighted_reg_oldglmfit_old
- weighted_reg_oldglmfit_old
- whole_brain_ewma
- whole_brain_ewma
- zero_crossing
- zero_crossing
CanlabCore/mlpcr
- cv_mlpcr.m
- cv_mlpcr.m
- cv_mlpcr3.m
- cv_mlpcr3.m
- cv_mlpcr3_bt.m
- cv_mlpcr3_bt.m
- cv_mlpcr3_wi.m
- cv_mlpcr3_wi.m
- cv_mlpcr_bt.m
- cv_mlpcr_bt.m
- cv_mlpcr_wi.m
- cv_mlpcr_wi.m
- mlpcr2
- mlpcr2
- mlpcr3
- mlpcr3
CanlabCore/peak_coordinates
- cluster_manova
- cluster_manova
- extract_ind_peak
- extract_ind_peak
- image2coordinates
- image2coordinates
- spatial_contrast
- spatial_contrast
CanlabCore/web_repository_tools
CanlabCore/External/circularGraph
CanlabCore/HRF_Est_Toolbox2/EstHRF_inAtlas
CanlabCore/Misc_utilities
Versions that use the GitHub default branch cannot be downloaded
Version | Published | Release Notes | |
---|---|---|---|
1.0.0 |
|
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