├── +bids ├── +internal │ ├── README.md │ ├── add_missing_field.m │ ├── append_to_layout.m │ ├── camel_case.m │ ├── create_unordered_list.m │ ├── download.m │ ├── ends_with.m │ ├── error_handling.m │ ├── file_utils.m │ ├── format_path.m │ ├── get_meta_list.m │ ├── get_metadata.m │ ├── get_version.m │ ├── is_github_ci.m │ ├── is_octave.m │ ├── is_valid_fieldname.m │ ├── keep_file_for_query.m │ ├── list_all_trial_types.m │ ├── list_events.m │ ├── match_structure_fields.m │ ├── nansum.m │ ├── parse_filename.m │ ├── plot_diagnostic_table.m │ ├── regexify.m │ ├── replace_placeholders.m │ ├── resolve_bids_uri.m │ ├── return_file_index.m │ ├── return_file_info.m │ ├── return_subject_index.m │ ├── root_dir.m │ ├── starts_with.m │ └── url.m ├── +transformers_list │ ├── Assign.m │ ├── BaseTransformer.m │ ├── Basic.m │ ├── Concatenate.m │ ├── Constant.m │ ├── Copy.m │ ├── Delete.m │ ├── Drop_na.m │ ├── Factor.m │ ├── Filter.m │ ├── Label_identical_rows.m │ ├── Logical.m │ ├── Mean.m │ ├── Merge_identical_rows.m │ ├── Product.m │ ├── Rename.m │ ├── Replace.m │ ├── Scale.m │ ├── Select.m │ ├── Split.m │ ├── Std.m │ ├── Sum.m │ ├── Threshold.m │ ├── check_field.m │ ├── coerce_fieldname.m │ ├── get_field_attribute.m │ ├── get_input.m │ ├── get_output.m │ ├── get_query.m │ ├── identify_rows.m │ ├── is_run_level.m │ └── miss_hit.cfg ├── +util │ ├── create_data_dict.m │ ├── create_participants_tsv.m │ ├── create_readme.m │ ├── create_scans_tsv.m │ ├── create_sessions_tsv.m │ ├── download_ds.m │ ├── jsondecode.m │ ├── jsonencode.m │ ├── jsonwrite.m │ ├── miss_hit.cfg │ ├── mkdir.m │ ├── plot_events.m │ ├── tsvread.m │ ├── tsvwrite.m │ └── update_struct.m ├── Contents.m ├── Description.m ├── File.m ├── Model.m ├── Schema.m ├── bids_matlab_version.m ├── copy_to_derivative.m ├── derivatives_json.m ├── diagnostic.m ├── functionSignatures.json ├── init.m ├── layout.m ├── query.m ├── report.m ├── transformers.m └── validate.m ├── .all-contributorsrc ├── .codespellrc ├── .editorconfig ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── blank.md │ ├── bug_report.yml │ └── feature_request.yml ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── auto_merge.yml │ ├── linkcheck.yml │ ├── run_examples.yml │ ├── run_tests_matlab.yml │ ├── run_tests_octave.yml │ ├── update_schema.yml │ └── validate.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .vscode └── settings.json ├── CITATION.cff ├── CONTRIBUTING.md ├── DECISION-MAKING.md ├── LICENSE ├── Makefile ├── README.md ├── binder ├── apt.txt ├── environment.yml └── postBuild ├── demos ├── .gitignore ├── notebooks │ ├── .gitignore │ ├── BIDS-Matlab_01_basics.ipynb │ ├── BIDS-Matlab_02_derivatives.ipynb │ ├── BIDS-Matlab_03_filenames_and_metadata.ipynb │ ├── BIDS-Matlab_04_new_datasets.ipynb │ ├── BIDS-Matlab_05_report.ipynb │ ├── BIDS-Matlab_06_tsv_json.ipynb │ ├── BIDS-Matlab_07_diagnostic.ipynb │ ├── BIDS-Matlab_08_stats_model.ipynb │ ├── BIDS_Matlab_01_basics.m │ ├── BIDS_Matlab_02_derivatives.m │ ├── BIDS_Matlab_03_filenames_and_metadata.m │ ├── BIDS_Matlab_04_new_datasets.m │ ├── BIDS_Matlab_05_report.m │ ├── BIDS_Matlab_06_tsv_json.m │ ├── BIDS_Matlab_07_diagnostic.m │ ├── BIDS_Matlab_08_stats_model.m │ ├── Makefile │ ├── add_bids_matlab_to_path.m │ ├── convert.py │ ├── miss_hit.cfg │ └── test_notebooks.m ├── spm │ ├── extract_confounds_fmriprep.m │ ├── facerep │ │ └── code │ │ │ ├── convert_facerep_ds.m │ │ │ └── spm_facerep.m │ └── moae │ │ └── code │ │ └── spm_moae.m ├── transformers │ ├── data │ │ └── sub-03_task-VisuoTact_run-02_events.tsv │ └── split_by_trials.m └── working_with_files.m ├── docs ├── Makefile ├── __pycache__ │ └── utils.cpython-312.pyc ├── add_links_to_changelog.py ├── commenting_images │ ├── BIDS_GitHub_mainpage.png │ ├── BIDS_comment.png │ ├── BIDS_comment_block.png │ ├── BIDS_file_comment.png │ ├── BIDS_pr.png │ ├── BIDS_pr_accept_comment.png │ ├── BIDS_pr_commit_batch.png │ ├── BIDS_pr_files_changed.png │ ├── BIDS_pr_list.png │ ├── BIDS_pr_reviewer_credit.png │ ├── BIDS_suggest.png │ ├── BIDS_suggest_change.png │ ├── BIDS_suggest_text.png │ └── gitflow_diagram.png ├── generate_doc.py ├── make.bat ├── requirements.txt ├── source │ ├── api │ │ ├── function_description.rst │ │ ├── index.rst │ │ └── utility_functions.rst │ ├── changelog.md │ ├── conf.py │ ├── contributing.md │ ├── demos.md │ ├── developper_doc │ │ ├── index.rst │ │ ├── maintenance.md │ │ └── private_api.rst │ ├── file.rst │ ├── general_information.md │ ├── images │ │ ├── MultisubjectMultimodalFaceProcessing.png │ │ ├── MultisubjectMultimodalFaceProcessing_splitby-task.png │ │ ├── Simon-task_func_Simontask.png │ │ ├── plot_events_ds001.png │ │ └── timing.png │ ├── index.rst │ ├── layout_query.rst │ ├── performance.rst │ ├── schema.rst │ ├── stats_model.rst │ └── variable_transformations.rst └── utils.py ├── miss_hit.cfg ├── npm-requirements.txt ├── package.json ├── requirements.txt ├── run_tests.m ├── schema.json ├── templates ├── README.md ├── README.template ├── README_datalad.template └── boilerplates │ ├── anat.tmp │ ├── credit.tmp │ ├── device_info.tmp │ ├── dwi.tmp │ ├── events.tmp │ ├── fmap.tmp │ ├── func.tmp │ ├── institution.tmp │ ├── meeg.tmp │ ├── mri_info.tmp │ ├── perf.tmp │ ├── pet.tmp │ ├── pet_info.tmp │ ├── physio.tmp │ └── task.tmp ├── tests ├── .gitignore ├── Makefile ├── bids-examples │ └── .gitkeep ├── create_dummy_data_set.py ├── data │ ├── bom_bug_552.tsv │ ├── dataset_description.json │ ├── model │ │ ├── model-balloonanalogrisktask_smdl.json │ │ ├── model-bug385_smdl.json │ │ ├── model-empty_smdl.json │ │ ├── model-narps_smdl.json │ │ └── model-rhymejudgement_smdl.json │ ├── reports │ │ ├── MoAE_all.md │ │ ├── asl003_perf.md │ │ ├── ds000117_anat.md │ │ ├── ds000117_dwi.md │ │ ├── ds000117_fmap.md │ │ ├── ds000117_func.md │ │ ├── ds000117_meg.md │ │ └── pet001_pet.md │ ├── sub-01_recording-autosampler_blood.tsv │ ├── sub-01_task-auditory_events.tsv │ ├── sub-01_task-auditory_events.tsv.gz │ ├── surface_data │ │ ├── sub-06_hemi-R_space-individual_den-native_midthickness.json │ │ ├── sub-06_hemi-R_space-individual_den-native_midthickness.surf.gii │ │ ├── sub-06_hemi-R_space-individual_den-native_thickness.json │ │ ├── sub-06_hemi-R_space-individual_den-native_thickness.shape.gii │ │ ├── sub-06_space-individual_den-native_thickness.dscalar.nii │ │ └── sub-06_space-individual_den-native_thickness.json │ ├── synthetic │ │ ├── CHANGES │ │ ├── README │ │ ├── T1w.json │ │ ├── dataset_description.json │ │ ├── derivatives │ │ │ ├── invalid_subfolder │ │ │ │ ├── dataset_description.json │ │ │ │ └── sub-01 │ │ │ │ │ └── _anat │ │ │ │ │ └── sub-01_desc-brain_mask.nii.gz │ │ │ └── manual │ │ │ │ ├── dataset_description.json │ │ │ │ └── sub-01 │ │ │ │ └── anat │ │ │ │ └── sub-01_desc-brain_mask.nii.gz │ │ ├── sub-01 │ │ │ ├── anat │ │ │ │ ├── sub-01_T1w.json │ │ │ │ └── sub-01_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-01_task-auditory_bold.json │ │ │ │ └── sub-01_task-auditory_bold.nii.gz │ │ ├── sub-ctrl01 │ │ │ └── anat │ │ │ │ └── sub-ctrl01_T1w.nii.gz │ │ ├── sub-test01 │ │ │ └── anat │ │ │ │ └── sub-test01_T1w.nii.gz │ │ └── task-auditory_bold.json │ └── tsv_files │ │ ├── sub-01_task-FaceRepetitionAfter_events.tsv │ │ ├── sub-01_task-FaceRepetitionBefore_events.tsv │ │ ├── sub-01_task-TouchAfter_events.tsv │ │ └── sub-01_task-TouchBefore_events.tsv ├── miss_hit.cfg ├── test_bids_description.m ├── test_bids_file.m ├── test_bids_init.m ├── test_bids_model.m ├── test_bids_schema.m ├── test_copy_to_derivative.m ├── test_derivatives_json.m ├── test_report.m ├── test_transformers │ ├── test_transformers.m │ ├── test_transformers_class.m │ ├── test_transformers_compute.m │ ├── test_transformers_munge.m │ └── test_transformers_side_functions.m ├── tests_layout │ ├── layout_timing.m │ ├── plot_timing.m │ ├── test_bids_examples.m │ ├── test_layout.m │ ├── test_layout_bugs.m │ ├── test_layout_derivatives.m │ ├── test_layout_index_json.m │ ├── test_layout_schemaless.m │ └── timing.tsv ├── tests_private │ ├── test_append_to_layout.m │ ├── test_error_handling.m │ ├── test_file_utils.m │ ├── test_get_metadata.m │ ├── test_get_metadata_suffixes.m │ ├── test_keep_file.m │ ├── test_list_all_trial_types.m │ ├── test_list_events.m │ ├── test_parse_filename.m │ ├── test_plot_diagnostic_table.m │ ├── test_replace_placeholders.m │ ├── test_resolve_bids_uri.m │ ├── test_return_file_index.m │ └── test_return_subject_index.m ├── tests_query │ ├── test_bids_query.m │ ├── test_bids_query_asl.m │ ├── test_bids_query_derivatives.m │ ├── test_bids_query_dwi.m │ ├── test_bids_query_eeg.m │ ├── test_bids_query_fmap.m │ ├── test_bids_query_func.m │ ├── test_bids_query_ieeg.m │ ├── test_bids_query_matlab_octave.m │ ├── test_bids_query_meg.m │ ├── test_bids_query_microscopy.m │ ├── test_bids_query_motion.m │ ├── test_bids_query_mrs.m │ ├── test_bids_query_nirs.m │ ├── test_bids_query_qmri.m │ └── test_query_bug_453.m ├── tests_slow │ ├── 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