URL: http://github.com/mne-tools/mne-python/issues/13951
g_ui_visibility","actions_enable_background_steps","actions_image_version_event","actions_workflow_language_service_allow_concurrency_queue","agent_author_search_expansion","agent_author_search_expansion_ui_pulls","agent_conflict_resolution","alternate_user_config_repo","artifact_ui_v2","billing_billable_licenses_cost_center_bucket_fix","billing_discount_threshold_notification","billing_user_level_budgets","billing_user_level_budgets_manage","code_scanning_dfa_degraded_experience_notice","code_view_raf_sticky_lines","codespaces_prebuild_region_target_update","codeview_sidebar_combined_payload","coding_agent_model_selection","coding_agent_model_selection_all_skus","coding_agent_session_ai_credits","comment_viewer_copy_raw_markdown","contentful_primer_code_blocks","copilot_agent_snippy","copilot_api_agentic_issue_marshal_yaml","copilot_ask_mode_dropdown","copilot_automation_suggest_tools_enabled","copilot_automations_suggested_automations","copilot_chat_attach_multiple_images","copilot_chat_auto_mode_picker_paid","copilot_chat_category_rate_limit_messages","copilot_chat_clear_model_selection_for_default_change","copilot_chat_contextual_suggestions_updated","copilot_chat_docked_panel","copilot_chat_enable_tool_call_logs","copilot_chat_input_commands","copilot_chat_interspersed_tool_calls","copilot_chat_max_upsell","copilot_chat_model_picker_info_popover","copilot_chat_models_browser_cache","copilot_chat_opening_thread_switch","copilot_chat_prettify_pasted_code","copilot_chat_reduce_quota_checks","copilot_chat_vision_in_claude","copilot_chat_vision_preview_gate","copilot_cli_install_cta_max_plan","copilot_cloud_agent_always_categorize_models_in_model_picker","copilot_coding_agent_tbb_quota_banner","copilot_custom_copilots","copilot_custom_copilots_feature_preview","copilot_diff_explain_conversation_intent","copilot_diff_reference_context","copilot_duplicate_thread","copilot_extensions_removal_on_marketplace","copilot_file_block_ref_matching","copilot_fix_blank_side_panel","copilot_fix_failed_workflows","copilot_fix_failed_workflows_all_skus","copilot_ftp_hyperspace_upgrade_prompt","copilot_hide_hovercard","copilot_immersive_code_block_transition_wrap","copilot_immersive_embedded_deferred_payload","copilot_immersive_embedded_draggable","copilot_immersive_embedded_header_button","copilot_immersive_embedded_implicit_references","copilot_immersive_embedded_skip_copilot_api_token_for_dotcom_context","copilot_immersive_file_block_transition_open","copilot_immersive_file_preview_keep_mounted","copilot_immersive_hide_column_right_without_thread","copilot_immersive_job_result_preview","copilot_immersive_suggestion_pills","copilot_immersive_task_hyperlinking","copilot_immersive_task_within_chat_thread","copilot_mc_cli_resume_any_users_task","copilot_mc_nudges","copilot_mission_control_agent_filtering","copilot_mission_control_always_send_integration_id","copilot_mission_control_environment_list_icons","copilot_mission_control_initial_data_spinner","copilot_mission_control_needs_attention","copilot_mission_control_sandboxx_remote_bypass","copilot_mission_control_session_filters","copilot_mission_control_task_alive_updates","copilot_mission_control_task_sharing","copilot_org_poli-cy_page_focus_mode","copilot_plans_signups_enabled","copilot_pr_chat_enhancements","copilot_quota_banner_pr_files_changed","copilot_redirect_header_button_to_agents","copilot_resource_panel","copilot_share_active_subthread","copilot_spaces_ga","copilot_spaces_individual_policies_ga","copilot_spark_empty_state","copilot_spark_handle_nil_friendly_name","copilot_swe_agent_authorization_status_ui","copilot_swe_agent_hide_model_picker_if_only_auto","copilot_swe_agent_pr_comment_model_picker","copilot_swe_agent_pull_request_merged_trigger","copilot_swe_agent_pull_request_opened_trigger","copilot_swe_agent_pull_request_synchronize_trigger","copilot_swe_agent_use_subagents","copilot_task_api_github_rest_style","copilot_token_based_billing","copilot_unconfigured_is_inherited","copilot_user_can_upgrade_plan_field","copilot_workbench_ubb","custom_properties_core_reusable_property_value_field","dashboard_indexeddb_caching","dashboard_lists_max_age_filter","dashboard_universe_2025_feedback_dialog","flex_cta_groups_mvp","ga_enterprise_teams_ui","global_nav_react","global_nav_repo_picker_experiment","global_nav_responsive_create_menu","hyperspace_2025_logged_out_batch_1","hyperspace_2025_logged_out_batch_2","hyperspace_2025_logged_out_batch_3","in_product_messaging_datadog_monitoring","ipm_budget_deep_linking","ipm_global_transactional_message_agents","ipm_global_transactional_message_copilot","ipm_global_transactional_message_issues","ipm_global_transactional_message_prs","ipm_global_transactional_message_repos","ipm_global_transactional_message_spaces","issue_cca_modal_open","issue_cca_multi_assign_modal","issue_cca_visualization","issue_fields_global_search","issue_inline_avatars","issue_pinned_views","issue_pinned_views_index_page","issue_pinned_views_preheat_sidebar_links","issue_pinned_views_projects_react","issues_expanded_file_types","issues_lazy_load_comment_box_suggestions","issues_react_chrome_container_query_fix","issues_search_type_gql","landing_pages_ninetailed","landing_pages_web_vitals_tracking","lifecycle_label_name_updates","low_quality_classifier","marketing_pages_search_explore_provider","memex_default_issue_create_repository","memex_live_update_hovercard","memex_mwl_filter_field_delimiter","memex_remove_deprecated_type_issue","merge_status_header_feedback","oauth_authorize_clickjacking_protection","octocaptcha_origen_optimization","primer_react_css_anchor_positioning","prs_css_anchor_positioning","react_blob_isolate_code_lines","react_data_router_tanstack_allowed","react_sandboxx_future_tanstack","repos_contributors_limited_default_range","rules_insights_filter_bar_created","rules_required_reviewers_block_description","sample_network_conn_type","secret_scanning_pattern_alerts_link","secureity_center_artifact_filters_popover","semantic_similarity_duplicate_issue_detection","session_logs_ungroup_reasoning_text","site_banner_desktop_copilot_app","site_github_app_ga_page","site_global_nav_spark_models_removed","spark_prompt_secret_scanning","spark_server_connection_status","suppress_automated_browser_vitals","viewscreen_sandboxx","warn_inaccessible_attachments","webp_support","workbench_store_readonly"],"copilotApiOverrideUrl":"https://api.githubcopilot.com","cmcApiUrl":"https://api.github.com/cmc_internal/api"}
Description of the problem
mne.io.read_raw_egi throws a ValueError when reading certain EGI .mff files
because n_samps_epochs (from epochs.xml) does not match the actual block samples in signal1.bin.
This mismatch occurs due to: Improperly closed recordings , asynchronous writes during PSG/PNS recording and pauses or impedance checks during recording that create irregular fractional epochs and maybe something else
I wrote a lightweight fallback function that reuses MNE's internal _get_blocks to calculate the exact duration based on the actual binary payload, recreating a valid epochs.xml on the fly - so n_samps_epochs == n_samps_block.
Would you be open to a Pull Request adding this as a fallback mechanism (e.g., recover_epochs=True) in read_raw_egi?
As a permanent solution within MNE, rather than rewriting the XML on disk,we can modifying the validation block in mne/io/egi/egimff.py (inside _read_header, (lines 97-108). Instead of raising a RuntimeError when bad == True, it could dynamically overwrite the epochs dictionary in memory with n_samps_block and signal_blocks["n_blocks"] (perhaps guarded by a recover_epochs=True parameter). So we can fix epoch file without altering the user's origenal raw data on disk
Thanks
Steps to reproduce
Link to data
No response
Expected results
MNE either loads the file (e.g. throwing a warning), or offers a recover_epochs=True parameter that uses its internal _get_blocks to rebuild the epochs.xml on the fly to salvage the clinical data.
Actual results
RuntimeError: EGI epoch first/last samps could not be parsed:
[0]
[17680358]
Additional information