| Name | bids-manager JSON |
| Version |
0.1.1
JSON |
| download |
| home_page | None |
| Summary | GUI application to manage BIDS datasets |
| upload_time | 2025-08-05 10:15:01 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
bids
dicom
gui
neuroimaging
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# BIDS Manager
**BIDS Manager** is a **PyQt-based** GUI that converts **DICOM** folders into **BIDS**-compliant datasets and allows easy metadata editing.
---
## 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` |
---
## Installation
You can install BIDS Manager in two ways:
### 1. One-click installers <sup>(recommended)</sup>
1. **Download** the ZIP package:
**[📦 One-click Installers](https://github.com/ANCPLabOldenburg/BIDS-Manager/raw/main/Installers/Installers.zip
)**
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` |
---
### 2. Install in a virtual environment (advanced)
```bash
# 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.
Raw data
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"description": "\n# BIDS Manager\n\n**BIDS Manager** is a **PyQt-based** GUI that converts **DICOM** folders into **BIDS**-compliant datasets and allows easy metadata editing.\n\n---\n\n## Requirements\n\n| Software | Minimum Version | Notes |\n|----------|-----------------|---------------------------------------------------------|\n| **Python** | 3.10 | Installed automatically if you use the one-click installers |\n| **Git** | \u2014 | Must be installed manually (see below) |\n\n### Installing Git\n\n| Platform | Command / Action |\n|-------------------|----------------------------------------------------|\n| **Windows** | Download and run the installer: <https://git-scm.com/download/win> |\n| **Ubuntu/Debian** | `sudo apt-get update && sudo apt-get install git` |\n\n---\n\n## Installation\n\nYou can install BIDS Manager in two ways:\n\n### 1. One-click installers <sup>(recommended)</sup>\n\n1. **Download** the ZIP package: \n **[\ud83d\udce6 One-click Installers](https://github.com/ANCPLabOldenburg/BIDS-Manager/raw/main/Installers/Installers.zip\n)**\n2. **Extract** the ZIP file and run the script for your operating system:\n\n| OS | Script | How to Run | Duration |\n|------------------|-------------------------------|------------------------------------|---------|\n| **Windows 10/11**| `install_bids_manager.bat` | Double-click | \u2248 5 min |\n| **Linux** | `install_bids_manager.sh` | `./install_bids_manager.sh` | \u2248 5 min |\n\n3. After the installation finishes, you will find two shortcuts on your desktop:\n\n| OS | Launch | Uninstall |\n|-------------|---------------------------|--------------------------------|\n| **Windows** | `run_bidsmanager.bat` | `uninstall_bidsmanager.bat` |\n| **Linux** | **BIDS Manager** (launcher)| `uninstall_bidsmanager.sh` |\n\n---\n\n### 2. Install in a virtual environment (advanced)\n\n```bash\n# 1. Create a virtual environment\npython3 -m venv <env_name>\n\n# 2. Activate it\nsource <env_name>/bin/activate # On Windows: <env_name>\\Scripts\\activate\n\n# 3. Install BIDS Manager from GitHub\npip install git+https://github.com/ANCPLabOldenburg/BIDS-Manager.git\n```\n\nThe package declares all dependencies including `heudiconv`, so installation\npulls everything required to run the GUI and helper scripts.\nAll core requirements are version pinned in `pyproject.toml` to ensure\nconsistent installations.\n\nAfter installation the following commands become available:\n\n- `bids-manager` \u2013 main GUI combining conversion and editing tools\n- `dicom-inventory` \u2013 generate `subject_summary.tsv` from a DICOM directory\n- `build-heuristic` \u2013 create a HeuDiConv heuristic from the TSV\n- `run-heudiconv` \u2013 run HeuDiConv using the generated heuristic\n- `post-conv-renamer` \u2013 rename fieldmap files after conversion\n- `bids-editor` \u2013 standalone metadata editor\n- `fill-bids-ignore` \u2013 interactively update `.bidsignore`\n\nAll utilities provide `-h/--help` for details.\n\n### Recent updates\n\n- The TSV produced by `dicom-inventory` can now be loaded directly in the GUI and\n its file name customised before generation.\n- The Batch Rename tool previews changes and allows restricting the scope to\n specific subjects.\n- A \"Set Intended For\" dialog lets you manually edit fieldmap IntendedFor lists\n if the automatic matching needs adjustment.\n- `run-heudiconv` now keeps a copy of `subject_summary.tsv` under `.bids_manager`\n and generates a clean `participants.tsv` using demographics from that file.\n- Re-running `run-heudiconv` on the same dataset now appends new subjects to\n the existing `.bids_manager` records and updates `participants.tsv` instead of\n overwriting them.\n- `dicom-inventory` distinguishes repeated sequences by adding `series_uid` and `rep`\n columns and records `acq_time` for each series in `subject_summary.tsv`.\n- Fieldmap rows for magnitude and phase images are now merged so each acquisition\n appears once with the combined file count, and their `series_uid` values are\n stored as a pipe-separated list so both sequences are converted.\n- `post-conv-renamer` now adds an `IntendedFor` list to each fieldmap JSON so\n fMRI preprocessing tools can automatically match fieldmaps with the relevant\n functional runs.\n- The GUI's Tools menu gained actions to refresh `_scans.tsv` files and edit\n `.bidsignore` entries.\n- The DPI scale dialog now adjusts values in 25% increments and the DPI button\n appears between the CPU and Authorship buttons.\n- On startup the GUI detects the system DPI and applies the matching scale.\n- The scanned data table now provides a \"Generate unique IDs\" button that\n assigns random 3\u2011letter/3\u2011digit identifiers to subjects. If an entry already\n exists for the same study in an existing `.bids_manager/subject_summary.tsv`,\n you are prompted to reuse its identifier.\n- A \"Detect repeats\" button can recompute repetition numbers based on\n acquisition time when all BIDS and given names are filled.\n\n",
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