Tutorial on scanning high-resolution EPI on SIEMENS scanners

This post lists the background material of the hands-on tutorial about high-resolution EPI on SIEMENS scanners.

Content and references during the tutorial

• 0:00 Introduction of this tutorial
• 0:57 Introduction to EPI
• 2:32 Data to download: OpenNeuro (brows to the Workshop files)
• 4:22 Optimized localizer for high-contrast T1: Pdfs of protocols
• 10:23 Access to hidden recon parameters in IceConfig
• 12:48 Changing IcePat parameters
• 16:32 GRAPPA regularization strengths: Blog post with further information
• 20:35 GRAPPA kernel size: Blog post with further information
• 28:03 Bandwidth of EPI: Blog post with further information
• 26:57 GRAPPA calibration data scheme: Paper on FLEET and FLASH GRAPPA
• 41:56 B0-related artifacts
• 47:03 Retrospective reconstruction
• 51:56 Phase correction algorithm: Blog post with further information
• 57:11 Magnitude phase and real part
• 58:18 Coil uncombined images
• 59:48 Acknowledgements

This tutorial is done in context of the 2019, Minnesota Workshop on Ultra high field MRI, Namely the Educational course on layer-fMRI organized by Cheryl Olman: https://www.cmrr.umn.edu/workshop2019/

The slides can be downloaded here: https://layerfmri.page.link/CMRR_2019_scanning

They are acquired at Scannexus and at SFIM.

The time series analysis shown in the slides was done in AFNI:
3dTstat -prefix MEAN.nii -mean overwrite Timeseries.nii'[0..$(2)]'
3dTstat -prefix tSNR.nii -tSNR overwrite Timeseries.nii'[0..$(2)]'

Other layer-fMRI tutorials:

• Tutorial on alignment of small coverage data to whole brain
• Tutorial on layer-fMRI VASO pipeline

Acknowledgments

• I thank Robin Heidemann for tips regarding the ImprovedGrappaWs and the GRAPPA Kernel size.
• I thank Markus Streicher for tips about the phase correction options.
• I thank Peter Koopmanns for tips regarding the PF reconstruction with POCS.
• I thank Kawin Setsompop for tips regarding the number of POCS iterations.
• I thank Jonathan Polimeni for tips about the regularization strength in the GRAPPA Kernel fit.
• I thank Andreas Schäfer for tips on complex values uncombined reconstruction.
• I thanks Sean Marrett for the inspiration to make this tutorial.
• I thanks Benedikt Poser for everything else.