Issues

• Provide an option to filter participants who only exist in BIDS rather than outright failing the bagel bids step

  flag:discuss
  Enhancement

  neurobagel/bagel-cli#733 · Filter by author surchs opened on Oct 9, 2026

• Question: Adding derivatives outside of Nipoppy

  _flag:stale
  Exploration

  neurobagel/bagel-cli#701 · Filter by author alyssadai opened on Jul 8, 2026
  3

• Consider accepting www URLs for URL fields in dataset_description.json

  _flag:staleusability
  Enhancement

  neurobagel/bagel-cli#684 · Filter by author alyssadai opened on Apr 29, 2026
  1

• Remove warning logic for BIDS-supported but not Neurobagel-supported data suffixes

  _flag:stalerefactor
  Enhancement

  neurobagel/bagel-cli#672 · Filter by author alyssadai opened on Mar 28, 2026
  1

• Test with empty BIDS table fails on pandas>=3

  dependencies_flag:stale
  Bug

  neurobagel/bagel-cli#671 · Filter by author alyssadai opened on Mar 27, 2026
  1

• Original TSV column order may not be respected for >1 columns mapped to a single-column variable

  flag:detail needed_flag:stale
  Bug

  neurobagel/bagel-cli#668 · Filter by author alyssadai opened on Mar 21, 2026
  1

• Switch to using bids-standard/python-validator for BIDS validation

  dependencies_flag:stalerefactor
  Exploration

  neurobagel/bagel-cli#655 · Filter by author alyssadai opened on Feb 24, 2026
  1

• Ensure imaging session paths stored by bagel bids reflect filesystem BIDS paths

  flag:discuss_flag:stale
  Bug

  neurobagel/bagel-cli#652 · Filter by author alyssadai opened on Feb 17, 2026
  3

• Support merging multiple pheno tsv/json pairs into one jsondb file for improved BIDS workflow

  flag:discuss_flag:staleusability
  Enhancement

  neurobagel/bagel-cli#650 · Filter by author dominikwelke opened on Feb 16, 2026
  1

• Match subject IDs between the BIDS table and phenotypic data with sub- prefix stripped

  somedayusability
  Enhancement

  neurobagel/bagel-cli#649 · Filter by author alyssadai opened on Feb 12, 2026

• issue with pip install bagel

  dependencies_flag:stale
  Bug

  neurobagel/bagel-cli#645 · Filter by author romainVala opened on Feb 5, 2026
  5

• Combine subcommands into one command

  flag:discuss_flag:staleusability
  Enhancement

  neurobagel/bagel-cli#638 · Filter by author alyssadai opened on Jan 20, 2026
  2

• Having to rerun the CLI for changes in the dataset description to take effect is inconvenient

  flag:discuss_flag:staleusability
  Exploration

  neurobagel/bagel-cli#636 · Filter by author alyssadai opened on Jan 19, 2026
  1

• Investigate running tests on CLI as a container

  _flag:stale
  Exploration

  neurobagel/bagel-cli#573 · Filter by author alyssadai opened on Oct 24, 2025
  1

• Consider expanding ISO8601 duration calculation to include days

  someday
  Enhancement

  neurobagel/bagel-cli#568 · Filter by author alyssadai opened on Oct 21, 2025

• Restore mutually exclusive treatment of healthy control vs other diagnoses

  flag:discuss_flag:stalerefactor
  Maintenance

  neurobagel/bagel-cli#528 · Filter by author alyssadai opened on Sep 8, 2025
  2

• Investigate speeding up CLI

  _flag:staleperformance
  neurobagel/bagel-cli#520 · Filter by author alyssadai opened on Aug 28, 2025
  1

• Consider renaming the docker image to bagel to match PyPI

  _flag:stale
  Exploration

  neurobagel/bagel-cli#519 · Filter by author surchs opened on Aug 27, 2025
  1

• Keep default NaN values when parsing BIDS table

  _flag:stalerefactor
  Maintenance

  neurobagel/bagel-cli#505 · Filter by author alyssadai opened on Aug 11, 2025
  2

• Support custom standardized variables

  flag:discuss_flag:stalemodelingsomeday
  Exploration

  neurobagel/bagel-cli#497 · Filter by author alyssadai opened on Aug 5, 2025
  3

• Cache fetched configuration namespaces and pipeline-catalog

  _flag:stalerefactorusability
  Enhancement

  neurobagel/bagel-cli#493 · Filter by author surchs opened on Jul 31, 2025
  2

• Add the CLI version and config (name + version) into the output jsonld

  flag:discuss_flag:stale
  Enhancement

  neurobagel/bagel-cli#492 · Filter by author surchs opened on Jul 31, 2025
  2

• Auto-release occasionally fails due to 403 unauthorized error

  _flag:staleprocess
  Bug

  neurobagel/bagel-cli#486 · Filter by author alyssadai opened on Jul 22, 2025
  1

• Automatically use .bidsignore in bids command when parsing a BIDS dataset

  someday
  Exploration

  neurobagel/bagel-cli#425 · Filter by author alyssadai opened on Jan 27, 2025
  1

• Turn generate_neurobagel_example_jsonlds.sh into makefile

  refactorsomedayusability
  Maintenance

  neurobagel/bagel-cli#412 · Filter by author alyssadai opened on Dec 19, 2024
  3