bids-manager 0.1.0

GUI application to manage BIDS datasets

BIDS Manager

BIDS Manager is a PyQt-based GUI that converts DICOM folders into BIDS-compliant datasets and allows easy metadata editing.

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Requirements

Software	Minimum Version	Notes
Python	3.10	Installed automatically if you use the one-click installers
Git	—	Must be installed manually (see below)

Installing Git

Platform	Command / Action
Windows	Download and run the installer: https://git-scm.com/download/win
Ubuntu/Debian	sudo apt-get update && sudo apt-get install git

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Installation

You can install BIDS Manager in two ways:

1. One-click installers ^{(recommended)}

1. Download the ZIP package:
   📦 One-click Installers
2. Extract the ZIP file and run the script for your operating system:

OS	Script	How to Run	Duration
Windows 10/11	install_bids_manager.bat	Double-click	≈ 5 min
Linux	install_bids_manager.sh	./install_bids_manager.sh	≈ 5 min

3. After the installation finishes, you will find two shortcuts on your desktop:

OS	Launch	Uninstall
Windows	run_bidsmanager.bat	uninstall_bidsmanager.bat
Linux	BIDS Manager (launcher)	uninstall_bidsmanager.sh

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2. Install in a virtual environment (advanced)

# 1. Create a virtual environment
python3 -m venv <env_name>

# 2. Activate it
source <env_name>/bin/activate          # On Windows: <env_name>\Scripts\activate

# 3. Install BIDS Manager from GitHub
pip install git+https://github.com/ANCPLabOldenburg/BIDS-Manager.git

The package declares all dependencies including heudiconv, so installation pulls everything required to run the GUI and helper scripts. All core requirements are version pinned in pyproject.toml to ensure consistent installations.

After installation the following commands become available:

• bids-manager – main GUI combining conversion and editing tools
• dicom-inventory – generate subject_summary.tsv from a DICOM directory
• build-heuristic – create a HeuDiConv heuristic from the TSV
• run-heudiconv – run HeuDiConv using the generated heuristic
• post-conv-renamer – rename fieldmap files after conversion
• bids-editor – standalone metadata editor
• fill-bids-ignore – interactively update .bidsignore

All utilities provide -h/--help for details.

Recent updates

• The TSV produced by dicom-inventory can now be loaded directly in the GUI and its file name customised before generation.
• The Batch Rename tool previews changes and allows restricting the scope to specific subjects.
• A "Set Intended For" dialog lets you manually edit fieldmap IntendedFor lists if the automatic matching needs adjustment.
• run-heudiconv now keeps a copy of subject_summary.tsv under .bids_manager and generates a clean participants.tsv using demographics from that file.
• Re-running run-heudiconv on the same dataset now appends new subjects to the existing .bids_manager records and updates participants.tsv instead of overwriting them.
• dicom-inventory distinguishes repeated sequences by adding series_uid and rep columns and records acq_time for each series in subject_summary.tsv.
• Fieldmap rows for magnitude and phase images are now merged so each acquisition appears once with the combined file count, and their series_uid values are stored as a pipe-separated list so both sequences are converted.
• post-conv-renamer now adds an IntendedFor list to each fieldmap JSON so fMRI preprocessing tools can automatically match fieldmaps with the relevant functional runs.
• The GUI's Tools menu gained actions to refresh _scans.tsv files and edit .bidsignore entries.
• The DPI scale dialog now adjusts values in 25% increments and the DPI button appears between the CPU and Authorship buttons.
• On startup the GUI detects the system DPI and applies the matching scale.
• The scanned data table now provides a "Generate unique IDs" button that assigns random 3‑letter/3‑digit identifiers to subjects. If an entry already exists for the same study in an existing .bids_manager/subject_summary.tsv, you are prompted to reuse its identifier.
• A "Detect repeats" button can recompute repetition numbers based on acquisition time when all BIDS and given names are filled.