This is the second blog post about graphic representations of cynical metaphors. The first post on graphical metaphors was about finding best layer-fMRI sequence and can be found here. This one is about how layer-fMRI fits into the landscape of other disciplines.Continue reading “The relationship of layer-fMRI with other fields: a graphical story in cynical metaphors”
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 “raw” dicom2nii-converted time-series are not BIDS compatible (see https://github.com/bids-standard/bids-specification/issues/1001).
The order of odd and even BOLD and VASO image TRs is dependent on the nii-converter.
Workarounds with 3D distortion correction, results in interpolation artifacts.
Workarounds without MOSAIC decorators result in impracticable large data sizes.
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.Continue reading “OHBM 2022 Hackathon project: MOSAIC for VASO fMRI￼”
This page collects layer-fMRI abstracts from neuro imaging conferences in 2022. This is following the tradition of layer-fMRI abstracts in the previous years: layer-fMRI abstracts 2019, layer-fMRI abstracts 2020, and layer-fMRI abstracts 2021. Comments and completions are welcome (email@example.com).Continue reading “Layer-fMRI abstracts 2022”
There are many sequences that have been proposed to be suited for layer-fMRI. This list includes GE-BOLD (Menon 1999), SE-EPI (Goense 2006), CPMG (Scheffler 2021), ASL (Kashyap 2021), diffusion fMRI (Truong 2009), 3D-GRASE (Moerel 2018), calibrated BOLD aka CMRO2 mapping (Guidi 2020), VASO (Hua 2013), phase regression (Stanley 2021), onset-time imaging (Yu 2014), depth-dependent deconvolution (Markuerkiaga 2021), CVR-calibration (Guidi 2016), and many more.
In this blog post, I want to summarise the take-home message from the seemingly never ending battle between researchers fighting about the best sequence for layer-fMRI. I seek to do so by means of cynical metaphors in graphical form. Because, why not. There are plenty more serious discussions already elsewhere1,2,3.Continue reading “Which sequence is best for layer-fMRI? A graphic story in cynical metaphors.”
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.”
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.
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”
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.”
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.
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.
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.
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.
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.
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.
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.
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.
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?
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
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
This post summarizes the presentation, tutorials, and discussions of the 2019 UHF Minnesota Workshop on Cortical Depth-Resolved fMRI Methods, Nov 12th-Nov 13th.
This page lists all open layer-fMRI job opportunities.
Suggestions are welcome to layerfMRI@gmail.com
- 2002 Post-doc position on layer-fMRI methods in Baltimore, USA with Jun Hua.
- 2022 Post-doc position on UHF high-resolution (f)MRI methods, Boston USA with Anna Blazejewska.
- 2022 PhD position on Laminar specific simultaneous Electroencephalography and Functional Magnetic Resonance Imaging in Epilepsy, At Kings college London, UK.
- 2022 PhD position opening on layer fMRI of prefrontal cortex at Roshan Cools lab in Nijmegen (Donders), Netherlands.
- 2022 PhD student position on layer-fMRI for surface perception. with Peter de Weerd, Maastricht Netherlands.
- 2022 PhD student Position on time resolved decoding and layer-fMRI with Peter Kok at UCL, London, UK.
- 2022 Staff scientists for NIH core facility that manages two 7Ts, Bethesda with Peter Bandettini.
- 2022 Fellow/senior researcher to work on 7T MRI tools, in Queensland Australia with Markus Barth.
- 2022 Postdoc position in Geneva starting in May 2022 with Olivier Reynaud on MRI methods development including layer-fMRI at their new 7T.
- 2022 Research Fellow at UCL (London) for 7T methods development with Guillaume Flandin(closing date is 30th April).
- 2021 Post doc postion with Floris de Lange in Nijmegen on Laminar Computations of Sensory Surprise.
- 2021 2 positions available at UC Berkeley / AMRIT with the NexGen 7T with David Feinberg: postdoc and a pulse sequence programmer.
- 2021 Assistant Researcher position to work on the Feinbergatron scanner in Berkeley, a 7T scanner build for the purpose of human layer-fMRI.
- 2021 Layer-fMRI post doc position on Cognitive Dopamine Function in Nijmegen, with Roshan Cools.
- 2021 Two post-doc positions on human layer-fMRI signal investigation and modeling at MGH with Jonathan Polimeni. [Post 1] and [Post 2].
- 2021 Max-Planck research group leader position (W2) on human layer-fMRI in Tuebingen Germany with Klaus Scheffler. And another one on animal models [here].
- 2021 PhD position available (now also for international students) from July 2022, in Queensland (AUS) with Markus Barth.
- 2021 A two year post-doc position available in Essen to work with the group of Nikolai Axmacher on laminar fMRI of the hippocampus. Deadline Oct 15th 2021.
- 2021 Two PhD positions on layer-(f)MRI with Markus Barth in Queensland, Australia. Deadline Aug 23rd 2021.
- 2021 Tenure research position on fMRI at ultra-high-fields with Nicolas Boulant, at Neurospin near Paris.
- 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 firstname.lastname@example.org for more information).
- 2020 Open Rank position in Illinois to work with a new 7T Terra system (Brad Sutton email@example.com 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. firstname.lastname@example.org
- 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