bids2dicom

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Robert Smith

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Apr 12, 2022, 9:22:27 PMApr 12
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Hi all,

I am working on a project that involves utilisation of many different BIDS Apps to perform image processing and more complex derivative generation.
Some of these data nevertheless need to be submitted via DICOM for radiological assessment (and our present duct tape solution for such will not support the ongoing evolution of our pipeline).

What I would ideally like is a software tool wherein the user specifies via configuration file the structure of the desired output DICOM study, and the input BIDS derivative data (or potentially DICOM / BIDS raw in some instances) from which each series should be constructed. This seems to me to be something that would potentially have wider community applicability.
  1. Has anyone out there already commenced work on such a tool?

  2. If we were to build something from scratch, would anyone out there be invested in contributing (whether in planning or implementation)?
    I already have something resembling a specification document of features I'd want, but external experience / learning of potential pitfalls or use cases would likely be useful here. And extra hands on deck would very much be welcomed.
Cheers
Rob

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Robert Smith, Ph.D
Senior Research Officer, Epilepsy Neuroinformatics Laboratory

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
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Heidelberg VIC 3084 Australia
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au

MRtrix3: Advanced tools for the analysis of diffusion MRI data
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Australian National Imaging Facility Fellow
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Ali Khan

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Apr 12, 2022, 9:51:15 PMApr 12
to bids-di...@googlegroups.com, Tristan Kuehn
Hi Rob,

We've made something simple like that recently, https://github.com/akhanf/snakebids2dicom
Uses a snakemake+pybids (snakebids) workflow and wraps a nifti2dicom tool that is out there (https://github.com/biolab-unige/nifti2dicom) setting uids and tags based on bids entities.

It's a bit stale as we haven't got around to using it much, and is based on an early version of snakebids, but we are happy to freshen it up and/or chat more about this use case in general.

Best,
Ali

From: bids-di...@googlegroups.com <bids-di...@googlegroups.com> on behalf of Robert Smith <robert...@florey.edu.au>
Sent: April 12, 2022 9:22 PM
To: bids-di...@googlegroups.com <bids-di...@googlegroups.com>
Subject: [bids-discussion] bids2dicom
 
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Sébastien Jodogne

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Apr 15, 2022, 9:08:40 AMApr 15
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Dear Robert,

We are actively working on the reverse strategy in the context of the Orthanc project for medical imaging [1], namely to transparently convert DICOM to BIDS on-the-fly.

This way, the DICOM instances are considered as the primary data, and are always available if the series must be sent to another DICOM modality (for instance for radiological assessment as you mentioned). BIDS is secondary data that is transparently generated on demand. In our work, Orthanc is used as an extensible, open-source PACS server that can centralize images received from any DICOM modality. Raw data to be associated with a BIDS study are stored as attachments to the DICOM series.

A plugin for Orthanc named "orthanc-neuro" will soon be available as free and open-source software. In its first version, the plugin will allow to convert any DICOM series to NIfTI by calling a REST API. Future versions will introduce the configurable, automated conversion to BIDS.

The use of an Orthanc plugin allows to get rid of the "duct tape pipelines" by directly embedding the NIfTI/BIDS conversion into the core of a robust DICOM server.

Kind Regards,
Sébastien-

Mutsaerts, H.J.M.M. (Henk Jan)

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Apr 18, 2022, 4:54:44 AMApr 18
to bids-di...@googlegroups.com, Wink, A.M. (Alle Meije), Kuijer, J.P.A. (Joost)
Dear Sébastien, Robert,


This sounds interesting, though I would say it is challenging to do this without a user interface, not all BIDS fields can be taken from the DICOMs alone.
Is there a chance we could try your work out using e.g., our multi-site EPAD data, including fMRI, DWI, ASL? This would be a good test of your work.

Best wishes,
Henk



Henk(-Jan) MM Mutsaerts, MD PhD
Amsterdam UMC/UZ Ghent/UCL
Phone: +31 6 4390 8284

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Sébastien Jodogne

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Apr 18, 2022, 5:04:30 AMApr 18
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Dear Henk,

Yes, indeed, it is definitely planned to have a Web user interface to configure the BIDS exports (NIfTI doesn't need this however).

I''ll keep you updated as soon as we have a beta version for BIDS available for testing. It is still unclear what types of modalities will be supported in this first version, but fMRI will most probably be our first target.

Kind Regards,
Sébastien-
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