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Changelog

Source: NEWS.md

BrainGnomes 0.7-3

  • 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

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.