BIDS 4 DICOM WG-16

Yaroslav O. Halchenko
@yarikoptic

Center for Open Neuroscience
Department of Psychological and Brain Sciences
Center for Cognitive Neuroscience
Dartmouth College
Live slides/Sources: https://datasets.datalad.org/centerforopenneuroscience/talks/2023-bids-dicom.html

Who am I?

Brief Bio

Born in Siberia (RSFSR, USSR), Grew up in Ukraine, Matured in U.S.A.

Standard for neural datasets: BIDS


Gorgolewski, K. J., Auer, T., Calhoun, V. D., Craddock, R. C., Das, S., Duff, E. P., Flandin, G., Ghosh, S. S., Glatard, T., Halchenko, Y. O., Handwerker, D. A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B. N., Nichols, T. E., Pellman, J., Poline, J.-B., Rokem, A., Schaefer, G., Sochat, V., Triplett, W., Turner, J. A., Varoquaux, G., and Poldrack, R. A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3:160044

BIDS ...

  • standardizes at the level of the dataset
  • is intended to be boring:
    You have seen one BIDS dataset -- you have seen them all!
  • is both human- and machine- friendly
    • From 1.7.0 WiP to make BIDS specification itself machine readable!
    • Schema avoids necessity for hard-coding BIDS in client software
  • compliance could be automatically verified using bids-validator BIDS-App
  • BIDS-Apps can process entire datasets given minimal specification
  • is enhanced through BIDS Enhancement Proposals (BEPs), e.g.
    • BEP028: Provenance (WiP)
    • BEP031: Microscopy (done)
    • BEP032: Animal electrophysiology (WiP)
    • ...
  • is a "meta-standard":

Bits of chronology/history

  • 1982 - DICOM initiation - 1st PACS Conference
    • PACS/DICOM - transmission and archival oriented
  • 1998 was the initiation of WG-16(?)
  • 199?s academic/.gov neuroimaging community started with dumbified “basic” file format Analyze (separate data + header) from Biomedical Imaging Resource (BIR) at Mayo Clinic
    • managing the multitude of DICOM files (mozaics etc) on drive (not in PACS) is not trivial
    • not all scanners produced them (Philips only in 201?)
    • Analyze is very simple, "not burdened" with metadata
    • Bob Cox (AFNI/lead of NIfTI effort)
      • DICOM doesn't store floats except as ASCII strings
      • The whole thing is so clumsy as to make battle hardened programmers recoil in fear
  • 2004 - Analyze successor NIfTI-1 is born
  • 2014 - BIDS born to organize NIfTI files + metadata in a dataset

NIfTI-1

https://nifti.nimh.nih.gov/nifti-1/documentation/hbm_nifti_2004.pdf/view

2017: State of things from an eye of DICOM ppl

https://www.dclunie.com/papers/MICCAI_2017_Clunie_DICOM.pdf

All standards are "Bad"*,
but some are used

* ref: D.Clunie, MICCAI 2017

2023:

We have two widely used standards,
which can benefit from cooperation

DICOMs in BIDS: the recommended source

DICOMs in BIDS: kept in "sourcedata/" for reconversion etc

e.g. visit http://datasets.datalad.org/?dir=/dbic/QA

DICOMs in BIDS: metadata extracted to .json

e.g. visit http://datasets.datalad.org/.../anat/sub-emmet_ses-20180531_acq-MPRAGE_T1w.json

How to "align"/enrich?

Q:How for us to collaborate on metadata important to academics?

  • Should we try individually channel to manufacturers or DICOM WGs could help?

Proposition/Q: Establish Common Work/Resources

  • library of concrete DICOM + BIDS conversions per manufacturer/data type/modality etc: BIDS Issues # 1350.
  • Encourage/Align work on WIPs (where aware/possible) such as e.g. Siemens Phisio data in DICOMs with BIDS + tools for conversion.

Thank you!

Let's discuss and stay in touch!