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

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:


  • 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.

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