OHBM 2022 Hackathon project: MOSAIC for VASO fMRI


Vascular Space Occupancy is an fMRI method that is popular for high-resolution layer-fMRI. Currently, the most popular sequence is the one by Rüdiger Stirnberg from the DZNE in Bonn, which is actively being employed at more than 30 sites.

Current users of the DZNE VASO sequence. Interactive map

This sequence concomitantly acquires fMRI BOLD and blood volume signals. In the SIEMENS reconstruction pipeline, these signals are mixed together within the same time series, which challenges its user friendliness. Specifically:
The “raw” dicom2nii-converted time-series are not BIDS compatible (see https://github.com/bids-standard/bids-specification/issues/1001).
The order of odd and even BOLD and VASO image TRs is dependent on the nii-converter.
Workarounds with 3D distortion correction, results in interpolation artifacts.
Workarounds without MOSAIC decorators result in impracticable large data sizes.

The goal of this Hackathon is to extend the 3D-MOSAIC to solve these constraints. This functor is commonly used to sort images by echo-times, by RF-channels, by magnitude and phase in the SIEMENS reconstruction pipeline into sets of mosaics . However currently, this functor does not yet support the dimensionality of SETs. In this project we seek to include SETs into the capabilities of the functor.

Meeting agenda

Zoom link: https://maastrichtuniversity.zoom.us/j/95060091475

Zoom meeting times:

  • Wednesday June 15th 14:00-15:30 (Amsterdam time), preparation meeting with Renzo (everyone welcome).
  • Thursday June 16th 14:00-15:30 (Amsterdam time), meeting with Renzo and Ben and everyone who want to join (probably about general ICE basics in VE).
  • Friday June 17th 14:00-15:30 (Amsterdam time), meeting with Renzo and Ben and everyone who wants to join (probably about specific questions of the MOSAIC functor).
  • Saturday June 18th 14:00-15:30 (Amsterdam time), meeting with Renzo (everyone is welcome).

Pre-Hackathon Pitch

Post-Hackathon Pitch

Example VASO dataset with proper BIDS-ification

Remi Gau, generated a template dataset that explains how to store layer-fMRI VASO data. This includes all the meta data for ‘raw’ and ‘derivative’ data.

Link to VASO fMRI BIDS demo: https://gin.g-node.org/RemiGau/ds003216/src/bids_demo

More pictures of the Hack


This project is based on previous tests by Rüdiger Stirnberg and Philipp Ehses to isolate the cause of the problem. This project will be based on the mosaic functor that was originally developed by Ben Poser and is currently being further extended by Philipp Ehses.
The compatibility of the “raw” data with BIDS are supported by BIDS extensions spear-headed by Remi Gau and supported by Daniel Handwerker.
The Hackathon logistics across various internet platforms are kindly guided by our Hackathon mentor Faruk Gulban.

I want to thank Chris Rodgers for his instructions of how to overwrite existing reconstuction binaries on the SIEMENS scanner without the need to reboot the entire system.

I want to thank David Feinberg, Alex Beckett and Samantha Ma for help testing the new reconstruction binaries at the Feinbergatron scanner in Berkley via remote scanning.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s