In this post I am collecting layer-fMRI abstracts of the main neuro imaging conferences.
This is following the tradition of layer-fMRI abstracts in the previous years:
Continue reading “layer-fMRI abstracts 2021”Author: renzohuber
Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers.
On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models.
This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020:
In this third event, it will be discussed how the layer-fMRI methodologies might be able to inform Cognitive models. The three speakers are researchers that are working to examine cognitive processes whose study is aided by understanding the structure and function of cortical layers. These cognitive processes could include memory, attention, learning, dreaming, language or cortical predictions (plus many, many more!)
Floris de Lange will give an overview of work done by his group to capture laminar fMRI activity changes in the visual cortex for prediction, attention and bottom-up input. André Bastos will present results of laminar LFP recordings and how feed-forward gamma-band and feedback alpha/beta band modulations help to understand cognitive effects including attention, working memory, and prediction processing. Michelle Moerel will talk about how computational models can be combined with laminar fMRI to understand human auditory processing.
Below you find the important links of the virtual event. Embedded videos of the talks, discussions, and a summary of the hot topics are going to be added on the day after the event.
Continue reading “Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers.”Brain QR Modem
Are you ever annoyed how hard it is to get brain data off the scanner? The fact that scanners usually contain private information about patients and are thus embedded in maximally restrictive clinical cyber-security environments, makes it quite complicated to get access to the data. Especially when visiting collaborative sites.
In this this Hackathon project, we aim to develop a purely uni-directional (safe) data streaming “hack” to transfer MRI data directly to the cloud by means dynamic QR codes.
In the early days of the Internet, modems (modulator-demodulator) were used to (i) convert digital information into audio streams, (ii) transfer them across telephone lines, and (iii) convert them back into the digital domain. Here, we aim to do the same thing with pixel data of MRI scans. However, instead of audio signal we will use machine-readable visual information: QR codes.
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Specific aims of the Brain QR modem
1.) We will develop an ICE-Functor that converts pixel data to QR codes in real time
2.) We will develop an Android app that converts the streamed QR coded into a series of png that are directly streamed to the cloud (Drive folder).
3.) We will develop a LayNii program that converts stacks of PNG images into Nii files.
This project contains many consecutive components of a modem. And will likely take 2-3 rounds of Hackathons to be completed.
Continue reading “Brain QR Modem”Baseline CBV and it’s role for the interpretation of layer-dependent VASO signals.
This blog post represents a continuation of the manuals regarding VASO acquisition and VASO signal analysis. It deals with the question of quantifying the VASO signal change with respect to the baseline blood volume at rest. In this post, I try to provide an overview of the values of baseline blood volume in the literature, I hypothesise reasons for their discrepancy and conclude by arguing that one should refrain from analyzing VASO in relative units after all.
Continue reading “Baseline CBV and it’s role for the interpretation of layer-dependent VASO signals.”Second Virtual Layer-fMRI ‘Dinner’: Laminae in the brain; fMRI vs. electrophysiology
On Sept 28th 2020, the second virtual layer-fMRI event is scheduled.
This meeting is held as a succession of the first virtual dinner in May 2020: https://layerfmri.com/virtualevent1/
In this second event, it will be discussed how the research field can bridge the gap between layer-dependent activity measures that are obtained with fMRI and electrophysiology, respectively. Kamil Ugurbil will present the perspective of high resolution for human neuroscience, Lucia Melloni will present the perspective of depth-dependent electrophysiological recordings in humans, and Seong-Gi Kim will talk about the combination of both worlds, layer-fMRI and layer-dependent electrophysiological recordings.
Below you find the important links of the the virtual event. Embedded videos of the talks, discussions, and a summary of the hot topics are going to be added on the day after the event.
2020 layer-fMRI abstracts
This page lists all of my favourite layer-fMRI conference abstracts from 2020.
OHBM, ISMRM, SFN abstracts are added as they are published. ISMRM will follow on July 24th.
FENS Webinar on Layer-fMRI
This blog post summarizes the FENS webinar entitled: Multiscale, multimethod human brain imaging. Organised by the Human Brain Mapping.
Organized by Lars Muckli and Lucy Petro.
Setting up LAYNII
The purpose of this blog post is to provide guidance on how to get started with the layer-fMRI analysis suite: LAYNII. This post is an extended version of the LAYNII README.
Meeting minutes of the virtual layer-fMRI event #1
On May 7th 2020, there was a virtual layerfMRI event to discuss current issues in the field.
This meeting was held as a replacement of an originally planned layer-fMRI dinner at ISMRM and happened in succession of an earlier in-person layerfMRI workshop in November 2019 (meeting minutes here).
Below you find the important links of the the virtual event, videos of the talks and discussions, and a summary of the hot topics that were discussed.
Continue reading “Meeting minutes of the virtual layer-fMRI event #1”
Equi-voluming: The Anakin Skywalker of layering algorithms
Authors: Renzo Huber and Faruk Gulban
When you want to analyze functional magnetic resonance imaging (fMRI) signals across cortical depths, you need to know which voxel overlaps with which cortical depth. The relative cortical depth of each voxel is calculated based on the geometry of the proximal cortical gray matter boundaries. One of these boundaries is the inner gray matter boundary which often faces the white matter and the other boundary is the outer gray matter boundary which often faces the cerebrospinal fluid. Once the cortical depth of each voxel is calculated based on the cortical gray matter geometry, corresponding layers can be assigned to cortical depths based on several principles.
One of the fundamental principles used for “assigning layers to cortical depths” (aka layering, layerification) is the equi-volume principle. This layering principle was proposed by Bok in 1929, where he tries to subdivide the cortex across little layer-chunks that have the same volume. I.e. gyri and sulci will exhibit any given layer at a different cortical depth, dependent on the cortical folding and volume sizes (see figure below).
With respect to applying equi-volume principle in layer-fMRI, the equi-volume layering has gone through quite a story. A plot with many parallels to Anakin Skywalker.
In this blog, the equi-volume layering approach is evaluated. Furthermore, it is demonstrated how to use it in LAYNII software.
Continue reading “Equi-voluming: The Anakin Skywalker of layering algorithms”
Quality assurance measures for layer-fMRI time series: How to obtain them in LAYNII
Doing layer-fMRI sometimes feels like doing nothing more than noise management. One must have a full grown masochistic personality trait to enjoy working with such messy data. Namely, layer-fMRI time series data suffer from each and every one of the artifacts in conventional fMRI; they are just much worse and there are also a few extra artifacts that we need to worry about. As such, layer-fMRI time series usually suffer from amplified ghosting, time-variable intermittent ghosting, non-gaussian noise, noise-coupling, motion artifacts, and signal blurring.
Thus, we need to have a set of metrics that tell us whether or not we can trust our specific data sets. We would like to have quality assessment (QA) tools that tell us when we need to stop wasting our time on artifact-infested data and throw them away. It would be extremely helpful to have tools that extract a basic set of QA metrics that are specifically optimized and suited for sub-millimeter resolution fMRI artifacts.
This blog post discusses a number of these layer-fMRI specific QA metrics and describes how to generate them in LAYNII.
Removing unwanted venous signal from GE-BOLD maps: Overview of vein removal models and implementations in LAYNII
Did you acquire a layer-fMRI study without VASO? Did you even acquire your data with GE-BOLD EPI? Don’t you know that this contrast is dominated by unwanted signals from locally unspecific large draining veins?
That’s ok. Don’t be down in the mouth. Nobody is perfect. It happens to the best of us 😉 Luckily, there are several models out there that should help you to tease out the tiny microvascular GE-BOLD signal that you care about and help you to remove the dominating macro-vascular venous signal. However, note that some of these vein-removal models work better than others. None of the models is perfect! But some of them are useful. The most relevant approaches are implemented in the LAYNII software suit on a voxel-wise level.
In this blog post, I want to describe these de-veining models and how to use them to get rid of unwanted macrovascular venous signals in LAYNII.
Referral to description of layerification algorithm in LN2_LAYERS
How can one assign layers to discrete voxels? Is it possible to perform topographical fMRI analyses across layers and columns directly in the original voxel space that raw data from the scanner come in?
Continue reading “Referral to description of layerification algorithm in LN2_LAYERS”
layer-fMRI Webinar MBIC 2020
Title: High resolution fMRI: An introductory course for data acquisition and analysis challenges.
Support: This lecture series is finanzially supported by the FPN-MBIC-school. The session on sequences and sequence artifacts is supported (in kind) by the York-Maastricht-partnership grant. Faruk Omer Gulban works for Brain Innovation.
Coordinators: Laurentius (Renzo) Huber & Omer Faruk Gulban, Cognitive Neuroscience Department
Email: renzohuber@gmail.com or faruk.gulban@maastrichtuniversity.nl
Dates: 7, 14, 21, 28 July 2020 (4 sessions in total), 3pm to 4:30pm.
Video Conference Zoom link (note that these sessions may be recorded): https://maastrichtuniversity.zoom.us/meeting/register/tJAvcu-qpj8sHNVD71Vcu95et-R14QKRs22T
Layer-fMRI VASO worldwide
This blog post gives an overview of the scientific network of researchers that are using the VASO (vascular space occupancy) for applications in layer-fMRI. I tried to give an overview of all layer-fMRI VASO papers published so far and provide a map of all layer-fMRI VASO labs around the globe. Continue reading “Layer-fMRI VASO worldwide”
Meeting Minutes of 2019 Minnesota workshop on Cortical Depth-Resolved fMRI Methods
This post summarizes the presentation, tutorials, and discussions of the 2019 UHF Minnesota Workshop on Cortical Depth-Resolved fMRI Methods, Nov 12th-Nov 13th.
Layer-fMRI Jobs
This page lists all open layer-fMRI job opportunities.
Suggestions are welcome to layerfMRI@gmail.com
- 2021 Post-Doc for layer-fMRI, in the Section of Functional imaging methods with Peter Bandettini, at NIH, Bethesda, USA.
- 2021 Research Scientists and/or Postdoctoral Researchers Position at the Laboratory for Consciousness (Hakwan Lau), in Riken Japan.
- 2021 PostDoc position to form om laminar-fMRI and EEG human fear extinction learning in Dortmund with Erhan Genç.
- 2021 Two PhD positions on layer-fMRI regarding auditory neuroscience with Federico De Martino in Maastricht.
- 2021 A PostDoc position on high resolution fMRI in non-human primates with Qi Zhu at NeuroSpin.
- 2021 A PostDoc position on laminar fMRI examining the role of feedback in human visual perception at the MPI in Tuebingen, Germany. (with Kiley Seymour)
- 2021 A Postdoc and a PhD position on mesoscale imaging in Magdeburg, Germany (Esther Kuehn)
- 2021 Two Postdoc positions for (layer-fMRI) methods development at UCL, UK, (Guillaume Flandin)
- 2020 Head of Imaging Core Facility in Juelich (with new 7T Terra scanner), Germany (ask Prof Weiss-Blankenhorn p.h.weiss@fz-juelich.de for more information).
- 2020 Open Rank position in Illinois to work with a new 7T Terra system (Brad Sutton bsutton@illinois.edu for more information).
- 2020 PhD position in Leipzig and Juelich on high resolution functional connectivity at 7T with Sofie Valk.
- 2020 Vadim Axelrod will host a postdoc for 7T layer-fMRI research in Israel. Applicable for PhD graduates from EU countries and Canada. vadim.axelrod@gmail.com
- 2020 3 Post doc positions at Freie Universitaet Berlin, on layer-fMRI. As part of ERC grant awarded to Radek Cichy.
- 2020 Faculty position for 7T in RIKEN (Japan)
- 2020 PhD student position to work in Maastricht with Federiko DeMartino on layer-fMRI in the auditory cortex.
- 2020 Post Doc or Pre Doc position at UCL with Callaghan, Nadine Grädel, Nadège Corbin, and Ali Aghaeifar on MRI methods, including layer-fMRI with VASO.
- 2020 Post Doc position in Leipzig (Max-Planck) on layer-specific real-time fMRI with Nick Weiskopf and Romy Lorenz.
- 2020 Post Doc position in Liege (Belgium) on high-resolution fMRI with Eveline Balteau and Christophe Phillips.
- 2020 Post Doc position in the new lab from Kawin Setsompop in Stanford US, on advanced (f) MRI acquisition and reconstruction. Also in collaboration with the Feinbergatron layer-scanner in Berkeley.
- 2020 Staff scientist position in the new lab from Kawin Setsompop in Stanford US, on advanced (f) MRI acquisition and reconstruction. Also in collaboration with the Feinbergatron layer-scanner in Berkeley.
- 2020 PhD position for layer fMRI in Maastricht with Rainer Goebel (Brain Innovations) and Renzo Huber.
- 2020 Post-doc on high-resolution fMRI at 7T with Alexander Puckett at the University of Queensland, Australia
- 2020 Layer-fMRI postdoc, with Nikolai Axmacher at Ruhr University Bochum
- 2020 Layer-fMRI postdoc, with Blake Butler, in London Ontario
- 2020 Lausanne, Switzerland, with Ileana Jelescu on diffusion functional fMRI at 7T
- 2020 Brisbane, Australia, with Alex Puckett, Post-doc and PhD positions, on layer-fMRI
- 2020 Trondheim, in Systems Neuroscience, Faculty Associate Professor with 7T
- 2020 Glasgow, with Jozien Goense on layer-fMRI applications, two post-docs and a faculty position.
- 2019 Suwon, Korea, with Kamil Uludag, Post-doc position on layer-fMRI methods.
- 2019 The Veterans Health Research Institute, with An Vu, about microscale fMRI
- 2019 Maastricht, with Benedikt Poser, Post-doc, on UHF advanced imaging.
- 2019 Glasgow, with Lars Muckli, on layerfMRI and computational modeling
- 2019 Magdeburg, with layerfMRI-expert Esther Kuehn, PdH-Position on Neuronal Mechanisms of Autosuggestion
- 2019 NIH, Bethesda, with Peter Bandettini, multiple positions on fMRI methods, including layerfMRI.
- 2019 UCSF, with Duan Xu, on advances imaging methods at with a GE 7T scanner, Post-doc position.
- 2019 Aalto, Finland, Faculty position on NeuroImaging (7T Terra might come soon).
- 2019 Montreal, with Rick Hoge at their new 7T Terra, Research Associate position on advanced UHF functional imaging.
- 2019 Liege, with 7T Terra, Post-doc MRI physicist
- 2019 Maastricht, with Federiko de Martino, on layer-fMRI, Post-doc
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.
Continue reading “Tutorial on scanning high-resolution EPI on SIEMENS scanners”
layer-fMRI abstracts
The following is a personal selection of my must-see layer-fMRI abstracts presented at SFN/OHBM/ISMRM. If I missed something, please let us know (layerfMRI@gmail.com).
SFN 2019 in Chicago
Saturday
- 4:00 pm – 5:00 pm, 092.12/ BB63. Poster, O. STANLEY, Phase-based macrovascular filtering from gradient echo bold fMRI reduces orientation dependence.
Sunday
- 8:00 am – 8:15 am, 111.01/Room S402. Nanosymposium talk, J. TOWNSEND: Non-invasive mapping of acoustic-phonetic speech features in human superior temporal gyrus using ultra-high field 7T fMRI.
- 11:00 am – 12:00 am, 141.04/K28. Poster, T. LIU: Affective processing of face stimuli in human primary visual cortex.
MP2RAGE: challenges and artifacts of its use for layer-fMRI
The MP2RAGE sequence is very popular for 7T anatomical imaging and is very commonly used to acquire 0.7-1 mm resolution whole brain anatomical reference data. Aside of this common application, it can also be very helpful for layer-fMRI studies to obtain even higher resolution T1 maps in the range of 0.5mm iso. However, when optimizing MP2RAGE sequence parameters for layer-fMRI studies, there are a few things that might be helpful to keep in mind.
In this post, I would like to discuss the challenges of using the popular MP2RAGE sequence in layer-fMRI studies. Specifically I will discuss challenges/features regarding:
- Background noise.
- Foldover artifact at very high resolutions.
- Usage of double-partial Fourier imaging.
- Inflow into arterial vessels.
Continue reading “MP2RAGE: challenges and artifacts of its use for layer-fMRI”
