Skip to main content

Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS)

Project description

Full documentation: https://bidscoin.readthedocs.io

BIDScoin Neurodesk Brain Imaging Data Structure (BIDS) GPL-v3.0 license Documentation status Pytest results DOI reference

BIDScoin is a user-friendly Python application suite that converts (“coins”) source-level (raw) neuroimaging data sets to standardized data sets that are organized according to the Brain Imaging Data Structure (BIDS) specification. Rather than depending on complex programmatic logic for source data-type identification, BIDScoin uses a mapping approach to discover the different source data types in your repository and convert them into BIDS data types. Different runs of source data are uniquely identified by their file system properties (e.g. file name or size) and by their attributes (e.g. ProtocolName from the DICOM header). Mapping information can be pre-specified (e.g. per site), allowing BIDScoin to make intelligent first suggestions on how to classify and convert the data. While this command-line procedure exploits all information available on disk, BIDScoin offers a Graphical User Interface (GUI) for researchers to check and edit these mappings – bringing in the missing knowledge that often exists in their heads only. This interactive step can also be skipped for employment in fully automated dataflow pipelines.

Data conversions are performed within plugins, such as plugins that employ dcm2niix, spec2nii or nibabel.

BIDScoin requires no programming knowledge in order to use it, but users can use regular expressions and plug-ins to further enhance BIDScoin’s power and flexibility, and readily handle a wide variety of source data types.

BIDScoin is developed at the Donders Institute of the Radboud University.

Features

  • [x] DICOM source data

  • [x] PAR/REC source data (Philips)

  • [x] NIfTI source data

  • [x] Physiological logging data*

  • [x] MR Spectroscopy data**

  • [x] PET/CT data

  • [x] Field maps*

  • [x] Multi-echo data*

  • [x] Multi-coil data*

  • [x] Plug-ins

  • [x] Stimulus/behavioural logfiles

    * = Only DICOM source data

    ** = Only Twix, SDAT/SPAR and P-file source data

How to contribute

Are you a Python programmer with an interest in BIDS who knows about GE and/or Philips data? Are you experienced with parsing stimulus presentation log-files? Or do you have ideas to improve BIDScoin or its documentation? Have you come across bugs? In any case, you are more than welcome to provide feedback and to contribute to this project.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bidscoin-4.6.2.tar.gz (699.7 kB view details)

Uploaded Source

Built Distribution

bidscoin-4.6.2-py3-none-any.whl (770.1 kB view details)

Uploaded Python 3

File details

Details for the file bidscoin-4.6.2.tar.gz.

File metadata

  • Download URL: bidscoin-4.6.2.tar.gz
  • Upload date:
  • Size: 699.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for bidscoin-4.6.2.tar.gz
Algorithm Hash digest
SHA256 91c1a48af0ab91953adfc248fc08165925b261d337a96ef4f8fbbeb0b00bdebe
MD5 e330097bf32eebbbae4c4b308d8d315a
BLAKE2b-256 c9a46ee8cc37c38542bf057aefa898fa461a5880f2e08f7209bfb7484a9c048b

See more details on using hashes here.

Provenance

The following attestation bundles were made for bidscoin-4.6.2.tar.gz:

Publisher: build-push-pypi.yml on Donders-Institute/bidscoin

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file bidscoin-4.6.2-py3-none-any.whl.

File metadata

  • Download URL: bidscoin-4.6.2-py3-none-any.whl
  • Upload date:
  • Size: 770.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for bidscoin-4.6.2-py3-none-any.whl
Algorithm Hash digest
SHA256 a51f7dc90715f390f38bc5f35ebab04cadfb6bc3857e299d72e01f145f9a4c6c
MD5 9097b322b376e706a3745d30881f8e44
BLAKE2b-256 7342b00adf6ffb697e92fa1c8b5cadf009ac86fa50d2582f76c3b1f609931561

See more details on using hashes here.

Provenance

The following attestation bundles were made for bidscoin-4.6.2-py3-none-any.whl:

Publisher: build-push-pypi.yml on Donders-Institute/bidscoin

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page