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BIDScoin: an easy toolkit to convert
your data into BIDS
Marcel Zwiers
The goal: Brain Imaging Data Structure (BIDS)
Software Sharing: BIDS appsData Sharing: BIDSData Source
Getting your data into BIDS should not be such a hard problem
Getting your data into BIDS should not be such a hard problem
Converting to BIDS: A mapping problem
User knowledge
1. It is not rule based but maps prior knowledge as well as individual user knowledge
- DICOM header information
- PAR(/REC) header information
- P*.7 header information
- Nifti header information
- File system information
- Plugin
2. The gathered information is stored in a flexible and human readable yaml file, the bidsmap
3. You can easily edit the yaml file / bidsmap to your needs
4. BIDScoin tools run automatically and require no programming knowledge
BIDScoin
Workflow
Step 1: Run the bidsmapper
usage: bidsmapper.py [-h] [-t TEMPLATE] [-n SUBPREFIX] [-m SESPREFIX]
sourcefolder bidsfolder
Step 2: Run the bidseditor
usage: bidseditor.py [-h] [-s SOURCEFOLDER] [-b BIDSMAP] [-t TEMPLATE]
bidsfolder
Step 3: Run the bidscoiner
usage: bidscoiner.py [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-f] [-s] [-b BIDSMAP] [-n SUBPREFIX] [-m SESPREFIX] [-v]
sourcefolder bidsfolder
Main window
Overview /
short worklist
Add user
knowledge
Template info
Edit window
DICOM
input
BIDS
output
 An open-source python toolkit that converts ("coins") source-level (raw)
neuroimaging data-sets to the BIDS standard
 The user does not need programming knowledge and can directly edit the mapping
with a GUI
 Institutes can provide their users with a custom template already containing the
mappings for the scans that are typically performed in the institute
 Tested over a broad spectrum of (DICOM) input data, including fieldmaps, mutli-
echo data, multi-coil data, PET scans and various kinds of anatomical, diffusion
and functional MRI scans.
BIDScoin
www.ru.nl/donders
https://github.com/Donders-Institute/bidscoin
Poster: W581
DICOM keys
BIDS values

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Ohbm 2019-lightningtalk-bid scoin

  • 1. BIDScoin: an easy toolkit to convert your data into BIDS Marcel Zwiers
  • 2. The goal: Brain Imaging Data Structure (BIDS) Software Sharing: BIDS appsData Sharing: BIDSData Source
  • 3. Getting your data into BIDS should not be such a hard problem
  • 4. Getting your data into BIDS should not be such a hard problem
  • 5. Converting to BIDS: A mapping problem User knowledge
  • 6. 1. It is not rule based but maps prior knowledge as well as individual user knowledge - DICOM header information - PAR(/REC) header information - P*.7 header information - Nifti header information - File system information - Plugin 2. The gathered information is stored in a flexible and human readable yaml file, the bidsmap 3. You can easily edit the yaml file / bidsmap to your needs 4. BIDScoin tools run automatically and require no programming knowledge BIDScoin
  • 7. Workflow Step 1: Run the bidsmapper usage: bidsmapper.py [-h] [-t TEMPLATE] [-n SUBPREFIX] [-m SESPREFIX] sourcefolder bidsfolder Step 2: Run the bidseditor usage: bidseditor.py [-h] [-s SOURCEFOLDER] [-b BIDSMAP] [-t TEMPLATE] bidsfolder Step 3: Run the bidscoiner usage: bidscoiner.py [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-f] [-s] [-b BIDSMAP] [-n SUBPREFIX] [-m SESPREFIX] [-v] sourcefolder bidsfolder
  • 8. Main window Overview / short worklist Add user knowledge Template info
  • 10.  An open-source python toolkit that converts ("coins") source-level (raw) neuroimaging data-sets to the BIDS standard  The user does not need programming knowledge and can directly edit the mapping with a GUI  Institutes can provide their users with a custom template already containing the mappings for the scans that are typically performed in the institute  Tested over a broad spectrum of (DICOM) input data, including fieldmaps, mutli- echo data, multi-coil data, PET scans and various kinds of anatomical, diffusion and functional MRI scans. BIDScoin