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Changelog

Source: NEWS.md

BrainGnomes 0.8-2

  • Refactor postprocessing to use job arrays and sentinels for cleanup
  • Add additional templates to prefetch needed by MRIQC

BrainGnomes 0.8-1

Released 2026-03-10

  • Improve CLI interface to support –help or BrainGnomes help
  • Add CLI status command to get project status from command line
  • Add dry_run option to run_project to see what would be run without executing it
  • Refactor prefetch to accept cohort specifications and extend them to T2w fetch.
  • Refactor prefetch to fall back to no desc field if desc:brain fails
  • Expand fMRIPrep TemplateFlow defaults to include MNI152NLin2009cAsym boldref, res-2 brain mask, brain probseg, and carpet dseg assets observed during workflow construction
  • Add conditional CIFTI TemplateFlow defaults so prefetch only stages MNI152NLin6Asym and fsLR sphere assets when fMRIPrep CLI options request --cifti-output
  • Harden prefetch caching and validation checks so that later failures invalidate skip logic
  • Make prefetch state query-specific so that an exact snapshot of templateflow files is retained
  • Move prefetch state files out of templateflow_home and into hashed project log paths; legacy state files in templateflow_home are now migrated and removed to avoid poisoning TemplateFlow standard-space discovery.
  • Expand TemplateFlow default to desc=None for T1w to mirror some versions of fmriprep.
  • Harden check on flywheel location to accommodate missing fw command.
  • Update RSQLite connections to default to synchronous=NULL to prevent spurious warnings
  • Included OASIS30 as a default template space for prefetch because it is used by fmriprep
  • bugfix: preserve cohort-<n> in BIDS parsing/reconstruction so postprocessing can resolve cohort-qualified fMRIPrep outputs such as space-MNIPediatricAsym_cohort-2

BrainGnomes 0.8

Released 2026-02-17

  • Add optional low-pass filtering of motion parameters before FD recomputation; rename notch config fields to bandstop_min_bpm/bandstop_max_bpm (deprecated: band_stop_min/band_stop_max).
  • All HPC jobs are now tracked in detail by an SQLite database
  • Job failures and other errors can now be investigated using diagnose_pipeline
  • Added a new vignette, “Diagnosing Pipeline Runs”, that walks through get_project_status(), get_subject_status(), and interactive use of diagnose_pipeline()
  • Improved error logging in HPC scripts so that success and failure are indicated more clearly
  • Stale .fail files are removed when a newer .complete file exists, clarifying status of processing steps
  • Jobs now write a manifest of files and times to the job tracking database for more thorough completeness tests
  • Added optional low-pass filtering of motion parameters, matching Gratton
  • Gracefully adjust motion filtering parameters if they fall above Nyquist at this TR
  • Modify extract ROIs config to avoid input_regex and always generate it internally from postproc stream
  • Add optional header row for postprocessed confounds TSVs, configurable via postprocess YAML and validated during setup
  • Added extensive checks on write/permission issues with directories and files
  • bugfix: Get CSF probseg image for MRIQC during prefetch
  • run_project() now skips TemplateFlow prefetch only when a prior successful prefetch covers requested spaces and the TemplateFlow manifest in job tracking still verifies; missing/deleted template files trigger re-prefetch.
  • bugfix: preserve user-specified metadata/log_directory (including external paths) instead of always resetting to <project_directory>/logs.
  • During postprocess setup, confound_calculate now offers guided prompts to add framewise_displacement when omitted, including whether to use motion-filtered FD and whether FD should be processed vs kept as noproc for QC/exclusion workflows.
  • Increase consistency of instructions and formatting in setup_project()
  • bugfix: avoid spurious “Already disconnected” warnings on exit from diagnose_pipeline()
  • bugfix: diagnose_pipeline() now respects configured metadata/log_directory instead of assuming <project_directory>/logs
  • bugfix: diagnose_pipeline() now matches subjects by exact sub-<id> tokens to avoid accidental partial matches
  • bugfix: run_bg_and_wait() now suppresses and restores ERR trap handling around wait, so non-zero container exits can be reconciled against success tokens before jobs are marked failed.
  • bugfix: shell trap handlers now attempt a best-effort SQLite status update to FAILED before exit, reducing _fail/DB mismatch after abrupt failures.
  • bugfix: update_tracked_job_status() now warns when no tracking rows are updated for a job_id (instead of failing silently).
  • bugfix: check_status_reconciliation() now checks .fail markers against DB status and reports mismatch details.

BrainGnomes 0.7-5

Released 2026-01-13

  • Add calculate_motion_outliers function to calculate motion outliers in a BIDS dataset
    • Returns mean FD alongside max FD
    • Includes task and run columns from BIDS info
    • Supports optional output_file argument to write results (CSV or TSV, with gzip support)
    • Defaults for notch filter: bandstop_min_bpm = 12, bandstop_max_bpm = 18 BPM
  • Use the scratch_directory for postprocessing images to avoid collisions and ensure that intermediates do not clog the output folder
  • Check that python packages directory is writable prior to attempting to resample a stereotaxic template to an image; fall back to a managed reticulate environment if not.
  • More robust postprocess logging (fallback log directory if requested location is unavailable) and clearer reporting of retained volumes during confound regression.
  • bugfix: 0 values for temporal filter cutoffs now disable the corresponding low/high-pass filter components.
  • bugfix: more complete handling of cases where confound calculate/regress is enabled, but no columns are specified.
  • bugfix: ROI extraction now writes empty connectivity outputs (with warnings) when all ROIs are dropped after filtering.
  • bugfix: add T2w to template pre-fetch so that fmriprep does not try to obtain this when users have T2w images
  • bugfix: correct regex in postprocessing step substitution when using user-specified order
  • bugfix: prevent spurious failure files for fMRIPrep/AROMA jobs that return non-zero exit codes despite successful completion

BrainGnomes 0.7-4

Released 2025-11-23

  • Add log messages for key R calls in pipeline, such as lmfit_residuals_4d
  • Implement log levels to allow user to control log detail when calling run_project
  • bug fixes for cases where confound calculate or confound regression are enabled, but no columns are specified
  • Add file lock mechanism to avoid race condition on reticulate setup in resample_template_to_img
  • bug fix for logger glue in run_fsl_command

BrainGnomes 0.7-3

Released 2025-11-11

  • bugfix: correctly handle unsigned integer data types in NIfTIs
  • lmfit_residuals_4d now handles partial (ala fsl_regfilt) and full regression and is used for applying AROMA
  • Nonaggressive and aggressive AROMA now supported
  • fsl_regfilt.R wrapper script removed from pipeline – all regression now happens with lmfit_residuals_4d
  • bugfix: args_to_df now tolerate multiple arguments after a hyphen
  • Added pre-fetch step for TemplateFlow files so that network access can be turned off inside singularity containers, avoiding socket errors that crop up within python’s multiprocessing module.
  • Amended PBS scripts to match current pipeline
  • TemplateFlow prefetch now runs via dedicated Slurm/PBS scripts that mirror other steps, including trapping and logging
  • bugfix: confound regression does not crash when scrubbing is disabled
  • bugfix: incorporate additional BIDS entities into location of confounds file

BrainGnomes 0.7-2

Released 2025-10-09

  • Allow min_vox_per_roi to be specified as a percentage or proportion of atlas voxels during ROI extraction
  • ROI extraction allows for an optional brain mask that is applied to the atlas and time series data
  • Add support for an explicit empty response (returns NA) in prompt_input when a default is provided
  • Support notch filtering of motion parameters prior to calculation of framewise_displacement
  • Support different head sizes for calculation of framewise displacement
  • run_project with force=TRUE enables overwrite for downstream operations, ensuring that steps are re-run
  • Persist location of non-standard YAML file locations when loading from file.
  • Pass through user-specified CLI to heudiconv, support overwrite and clearing the cache
  • bugfix: look for MNI152NLin6Asym_res-2 recursively when verifying readiness for AROMA

BrainGnomes 0.7-1

Released 2025-09-24

  • UI/UX improvements to ask query enable/disable for postprocessing and ROI extraction during edit_project
  • Do not ask about ROI extraction details if no postprocessing streams are defined
  • Corrected validation of band-pass cutoffs and clarified temporal filtering prompts/documentation
  • Improved log messages related to temporal filtering

BrainGnomes 0.7

Released 2025-09-16

  • Tested and vetted flywheel sync
  • Defer subject processing loop when flywheel sync is the first step
  • validate_project adds argument correct_problems to prompt user for corrections if requested
  • run_project does not continue if no steps are requested
  • check that the scratch_directory is writable when the project is loaded and prompt for a new directory if not
  • bugfix: validate_project does not return a top-level ‘gap’ for postprocess when config is valid
  • bugfix: edit_project allows enable/disable modifications
  • bugfix: edit_project looks for missing config settings when enabling a previously disabled step
  • bugfix: do not display postproc or extract menus when filling in configuration gaps

BrainGnomes 0.6-1

Released 2025-09-04

  • Added Rcpp automask function, mimicking AFNI 3dAutomask.
  • Use automask to get approximate whole-brain mask for image quantiles in postprocessing (spatial_smooth, intensity_normalize)
  • Use the user-specific mask file in apply_mask, if relevant
  • Added prompt_directory, which asks for confirmation when user specifies a non-existent directory
  • Support use of AROMA in postproc for outputs generated by fmriprep 23 and before

BrainGnomes 0.6

Released 2025-08-30

  • Added ROI extraction workflow (extract_rois) with correlation options and a dedicated vignette.
  • Introduced a Flywheel synchronization step for retrieving data.
  • Added support for external BIDS and fMRIPrep directories, including an is_external_path helper, path normalization, and configurable postproc_directory.
  • Enhanced postprocessing: new output_dir argument, direct output movement without symlinks, robust file handling, and optional AROMA cleanup with safety checks for MNI res-2 outputs.
  • Refined project setup and validation by verifying directories before saving, prompting for required containers, and allowing projects to run without a postprocessing directory.
  • Documentation and test improvements, including an expanded quickstart guide and instructions for building the FSL container.