
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.09.04.611294
preprint
1
Article
Fuzzy ripple artifact in high resolution fMRI: identification, cause, and mitigation
Huber Renzo http://orcid.org/0000-0002-3291-2202

Stirnberg Rüdiger http://orcid.org/0000-0001-7021-1063

Morgan A Tyler http://orcid.org/0000-0001-6017-2179

Feinberg David A http://orcid.org/0009-0002-5016-9165

Ehses Philipp http://orcid.org/0000-0002-5839-6525

Knudsen Lasse
Gulban Omer Faruk http://orcid.org/0000-0001-7761-3727

Koiso Kenshu http://orcid.org/0000-0001-5931-6294

Swegle Stephanie http://orcid.org/0009-0002-6579-3972

Gephart Isabel
Wardle Susan G http://orcid.org/0000-0003-2216-7461

Persichetti Andrew http://orcid.org/0000-0002-1580-8497

Beckett Alexander JS http://orcid.org/0000-0002-7123-9559

Stöcker Tony http://orcid.org/0000-0002-8946-9141

Boulant Nicolas http://orcid.org/0000-0003-2144-2484

Poser Benedikt A http://orcid.org/0000-0001-8190-4367

Bandettini Peter http://orcid.org/0000-0001-9038-4746

09 9 2024
2024.09.04.611294https://creativecommons.org/publicdomain/zero/1.0/ To the extent possible under law, the person who associated CC0 with this work has waived all copyright and related or neighboring rights to this work.
http://biorxiv.org/lookup/doi/10.1101/2024.09.04.611294
nihpp-2024.09.04.611294.pdf
Abstract

Purpose

High resolution fMRI is a rapidly growing research field focused on capturing functional signal changes across cortical layers. However, the data acquisition is limited by low spatial frequency EPI artifacts; termed here as Fuzzy Ripples. These artifacts limit the practical applicability of acquisition protocols with higher spatial resolution, faster acquisition speed, and they challenge imaging in lower brain areas.

Methods

We characterize Fuzzy Ripple artifacts across commonly used sequences and distinguish them from conventional EPI Nyquist ghosts, off-resonance effects, and GRAPPA artifacts. To investigate their origin, we employ dual polarity readouts.

Results

Our findings indicate that Fuzzy Ripples are primarily caused by readout-specific imperfections in k-space trajectories, which can be exacerbated by inductive coupling between third-order shims and readout gradients. We also find that these artifacts can be mitigated through complex-valued averaging of dual polarity EPI or by disconnecting the third-order shim coils.

Conclusion

The proposed mitigation strategies allow overcoming current limitations in layer-fMRI protocols:

Achieving resolutions beyond 0.8mm is feasible, and even at 3T, we achieved 0.53mm voxel functional connectivity mapping.

Sub-millimeter sampling acceleration can be increased to allow sub-second TRs and laminar whole brain protocols with up to GRAPPA 8.

Sub-millimeter fMRI is achievable in lower brain areas, including the cerebellum.
==== Body
pmc
