search

ohbm / hackathon2022

Website for the 2022 OHBM Hackathon
https://ohbm.github.io/hackathon2022/
MIT License
5 stars 11 forks source link

MOSAIC for VASO fMRI #42

Open layerfMRI opened 2 years ago

layerfMRI commented 2 years ago

Title

MOSAIC for VASO fMRI

Short description and the goals for the OHBM BrainHack

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.

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 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.

Acknowledgements:

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.

Link to the Project

https://layerfmri.com/hackathon22/

Image for the OHBM brainhack website

https://layerfmri.files.wordpress.com/2022/05/image-01.png

Project lead

Twitter handle: @layerfmri, Name: Renzo Huber, Discort Handle: renzohuber #8546 Twitter handle: @ofgulban, Name: Omer Faruk Gulban,

Main Hub

Europe / Middle East / Africa

Other Hub covered by the leaders

Skills

Recommended tutorials for new contributors

Good first issues

Reconstructing an example TWIX files from raw k-space data to images. Understanding the logistics of the MOSAIC functor in his current form.

Twitter summary

We are extending the MOSAIC functor in SIEMENS MRI reconstruction to support concomitantly acquired VASO and BOLD with BIDS compatibility. @layerfmri @ofgulban @mriphilipp @HighOnField @RemiGau

Short name for the Discord chat channel (~15 chars)

VASO-MOSAIC

Please read and follow the OHBM Code of Conduct

djarecka commented 2 years ago

could you please provide leader's names. Did you register to discord?

djarecka commented 2 years ago

I removed the image from the description, hope that's fine

layerfMRI commented 2 years ago

The name is included now: Twitter handle: @layerfmri, Name: Renzo Huber, Discortd handle: renzohuber #8546 Including the Discord username.

djarecka commented 2 years ago

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides! If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)

layerfMRI commented 2 years ago

Thanks, Please find the slide here: https://docs.google.com/presentation/d/1jdt0agScrEZAqIFh-2q059y7yCF9iphT/edit?usp=sharing&ouid=118282357829216387805&rtpof=true&sd=true

I hope I will figure out how the present virtually by then.

Remi-Gau commented 2 years ago

Work in progress: creating BIDS compatible VASO dataset

https://gin.g-node.org/RemiGau/ds003216/src/bids_demo