On August 22nd 2024, we will host the 7th virtual layer-fMRI dinner. As usual, it’s free, just follow the link below.
The 7th layer-fMRI dinner will focus on Translational Applications of layer-fMRI.
For pages of previous dinners see here: https://layerfmri.com/dinners/
Continue reading “Seventh layer-fMRI dinner: Translational Applications of layer-fMRI.”Authors: รmer Faruk Gรผlban, Renzo Huber | Date: April 2024
Chapter published here: https://www.sciencedirect.com/science/article/abs/pii/B9780128204801001881
Functional magnetic resonance imaging (fMRI) today is a common method to study the human brain. The popularity of fMRI can be explained by its versatility and accessibility to study the structure-function relationship in living humans, which has historically been challenging or impossible. One area of constant progress and excitement since the early days in fMRI is the advances in hardware, MR sequences, and software which allowed researchers to image the fine details of the human brain non-invasively. fMRI is currently capable of reaching sub-millimeter resolution, effectively transforming the MRI scanner from a macroscope into a mesoscope. While 0.8 mm isotropic voxel resolution (~0.5 ฮผl) has become a part of the daily routine of a high resolution fMRI researcher at 7 Tesla scanners, as opposed to e.g. 3 mm isotropic voxels in conventional fMRI studies conducted at 3 T (Bollmann et al. 2020), recent developments have breached 0.37 mm isotropic resolution (~0.05 ฮผl) (Feinberg et al. 2023). This 10 fold reduction in voxel volume promises an exciting future to observe the fine mesoscopic details such as cortical layers, columns, and vessels during changes in human brain function.
Continue reading “Computing geometric layers and columns on continuously improving human (f)MRI data”
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 Rรผdiger 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 โrawโ 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๏ฟผ”This post is part of a series on graphical metaphors (continue here).
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.”In this post collects layer-fMRI abstracts of the main neuroimaging conferences. This is following the tradition of layer-fMRI abstracts in the previous years: layer-fMRI abstracts 2019, layer-fMRI abstracts 2020
Continue reading “layer-fMRI abstracts 2021”
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. Andrรฉ 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 โDinner’: Cognitive Models and Cortical Layers.”Bi-weekly discussions on current developments in layer-specific functional MRI: sequences, hardware, data acquisition, analysis methods, cognitive and vascular neuroscience, and mesoscale brain connectivity.
Complete list of all seminars, including past presentations. Click on speaker names or topics for links to full papers and recordings.
| ๐ Date | ๐ค Speaker | ๐ Topic |
|---|---|---|
| Dec 21, 2026 | โ | Winter break โ No Meeting |
| Dec 7, 2026 | Gordon Smith | Common principles underlying the development of large-scale cortical networks. |
| Nov 23, 2026 11 AM | Jingnan Du | Imaging cortical networks with precision |
| Nov 9, 2026 | Joseph Emerson | Orientation-tuned surround suppression exhibits a unique laminar signature in the human primary visual cortex. ๐ Paper |
| Oct 26, 2026 | ISMRM Submitters | Abstract feedback and discussion (deadline Oct 28) |
| Oct 12, 2026 | โ | ๐๏ธ Indigenous Peoples’ Day โ No Meeting |
| Sept 28, 2026 | Johannes Franz | Cortical myeloarchitectural types in a 75 ฮผm isotropic whole human brain ex-vivo dataset |
| Sept 14, 2026 | Nadine Graedel | High-Resolution BOLD fMRI at 7T in Regions of High Field Inhomogeneity |
| Aug 31, 2026 | Xin Yu Tyler Morgan | Neuronal Activity Related Sodium (NARS)-fMRI: Quantum Ionic Brain Mapping with Spin-3/2 ยฒยณNa Relaxation Functional sodium MR reveals neuronal responses in humans |
| Aug 17, 2026 | Antonia Massmann | The development of sensory processing in the human infant brain |
| Aug 3, 2026 | Saskia Bollmann | First impression of the Terra.X Impulse MRI scanner for precision neuroscience research |
| July 20, 2026 | โ | โ๏ธ Summer Break |
| July 6, 2026 | Tommy Clausner | Frequency and Laminar Profile of Feature Specific Activity Revealed by EEG-fMRI |
| June 22, 2026 | Daniel Haenelt | Removing the effect of macro-vascular veins from mesoscale fMRI |
| June 8, 2026 | Yuhui Chai | Resolving mesoscale brainstem-prefrontal-striatal pathways underlying decisions upon salient events using submillimeter-resolution fMRI ๐บ |
| May 25, 2026 | โ | ๐๏ธ Holiday |
| May 11, 2026 | โ | Canceled โ ISMRM Conference |
| April 27, 2026 | Renzo, Allessandra | ISMRM Rehearsal Presentations |
| April 13, 2026 | Lasse Knudsen | Latest progress of high-res fMRI at 10.5T |
| March 30, 2026 | Suvi Hรคkkinen | Functional imaging of hippocampal layers using VASO on the Next Generation (NexGen) 7T |
| March 16, 2026 | Wietske van der Zwaag | Mesoscale (f)MRI of the Cerebellum |
| March 2, 2026 | โ | Canceled by speaker |
| Feb 16, 2026 | โ | Presidents’ Day โ No Meeting |
| Feb 2, 2026 | Dana Ramadan | Macrovascular contributions to resting-state fMRI signals: A comparison between EPI and bSSFP at 9.4 Tesla |
| Jan 19, 2026 | โ | Shifted by speaker request |
| ๐ 2025 Events | ||
| Dec 8, 2025 | Saskia Bollmann | Towards Quantitative Analysis of Vascular Characteristics in the Human Brain |
| Nov 24, 2025 | Alejandro Monreal | Layer-fMRI spirals: VASO fMRI spirals, 11.7T fMRI spirals, etc. |
| Nov 10, 2025 | Omer Faruk Gulban | Meso-vessel imaging with 7 T MRI: Linking anatomy and function in living humans |
| Oct 27, 2025 | Renzo Huber Divya Varadarajan Alessandra Pizzuti | PNS Optimized Pulses for EPI (POPE): Simple adjustment to gradient pulse shape for practical high-resolution fMRI SurfScribe: Cortical surfaceโdriven automated online slice prescription applied to ultra-high-resolution vascular MRI LN2_FRISGO: A software solution for artifact mitigation in fast high-resolution fMRI Layer-fmri at 0.4 mm isotropic: Partners or Confounders with vascular mapping (0.35 mm iso)? |
| Oct 13, 2025 | CMRR Workshop | Hands-on Layer-fMRI Analysis Course โ LayNii, FreeSurfer, BrainVoyager (Luca Vizioli, Renzo Huber, Jonathan Polimeni, Rainer Goebel) |
| Sept 29, 2025 | Shahin Nasr | Mesoscale cortical plasticity in humans revealed by high-resolution functional MRI |
| Sept 15, 2025 | Amelia Strom | Quantification of cerebral cortical displacement driven by visual stimulation using motion-encoded stimulated-echo EPI at 7T |
| Sept 1, 2025 | โ | Labor Day โ No Meeting |
| Aug 18, 2025 | Sharif Kronemer | The human brain mechanisms of afterimages: From networks to cortical layers |
| Aug 4, 2025 | Marianna Schmidt | Mesoscale functional connectivity within the human primary visual cortex |
| June/July 2025 | โ | Summer Break |
| May 27, 2025 | Faruk Gulban | Faster, Finer, Higher, Larger with LayNii IDA: Meso Veins Meet Layer fMRI |
| May 12, 2025 | โ | Canceled โ ISMRM Hawaii |
| April 28, 2025 | Stephanie, Khazar, Renzo, Marco | ISMRM Mock Presentations โ Dynamic CSF volume imaging, 3rd order shim, layer-fMRI in hippocampus, layer-toolbox |
| April 14, 2025 | Elisa Zamboni | Mapping Curvature Domains in Human V4 Using CBV-Sensitive Layer-fMRI at 3T |
| March 31, 2025 | โ | Canceled โ ISMRM Workshop Annapolis |
| March 17, 2025 | Gabi Lohmann | Cylarim: A new tool for laminar-specific fMRI analysis |
| March 3, 2025 | Fraser Aitken | Layer-fMRI and Epilepsy |
| Feb 17, 2025 | โ | Presidents’ Day โ No Meeting |
| Feb 3, 2025 | Renzo Huber | Updates on EPI Artifact Mitigations โ Towards whole brain layer-fMRI with faster TRs |
| Jan 22, 2025 10:30 AM | Emma Brouwer | Cerebellar Imaging using 7T MRI |
| ๐ 2024 Events | ||
| Dec 13, 2024 | Burak Akin | Layer-fMRI Patch Analysis โ Looking for instantaneous layer profiles |
| Nov 29, 2024 | Ethan Buch | Layer-fMRI VASO on motor learning (Leo Cohen’s lab) |
| Nov 15, 2024 | โ | Canceled โ SFN Conference in DC |
| Nov 1, 2024 | Group Discussion | ISMRM Abstract Submissions (10:30โ11:30 AM) |
| Oct 18, 2024 | Kenny Chung | T1234 EPI โ Discussion of ISMRM submissions (10:30โ11:30 AM) |
| Oct 4, 2024 | โ | Canceled โ Boston Workshop on Layer-fMRI |
| Sept 20, 2024 | Group | Rehearsal Talks for Boston Layer-fMRI Workshop (10:30โ11:30 AM) |
| Sept 6, 2024 | Grant Hartung | Capillary Density Induces “Microvascular Biases” in Layer-fMRI BOLD โ Insights from realistic vascular modeling |
| Aug 23, 2024 | โ | Canceled โ Summer Holidays |
| July 26, 2024 | Jiajia | Layer-specific finger representations in human area 3b โ OHBM abstract |
| June 28, 2024 | Silvina Horovitz | High-resolution VASO in focal hand dystonia patients (30 min earlier) |
| June 14, 2024 | Renzo Huber | ISMRM Post-Discussion |
| May 31, 2024 | Renzo, Yuhui | ISMRM Rehearsal โ Fuzzy Ripples talk and Recent Advances in Layer-fMRI, VAPER connectivity |
| May 17, 2024 | Daniel Zaldivar | Layer-dependent changes of neural activity underlying laminar fMRI |
| May 3, 2024 | Faruk Gulban | Tutorial: ITK-SNAP Segmentation โ Video |
| April 19, 2024 | Tyler | Cortical-subcortical connection overview |
| April 5, 2024 | Sam Audrain, Andrew Persicetti | Capturing layer-fMRI in inferior parts of the cortex |
| March 22, 2024 | Eli Meriam | Informal discussion โ Future layer-fMRI study on texture processing in V1/V2 |
| March 8, 2024 | Aneurin Kennerley | DIANA โ Human line scanning at 3T |
| Feb 22, 2024 | Atena Akbari | Phase-regression and VASO for layer-fMRI in ocular dominance columns |
| Feb 8, 2024 | Jun Hua | Layer-fMRI with memory encoding in the entorhinal cortex |
| Jan 25, 2024 | Sohuyn Han | Spin-Echo BOLD for Improved Layer-Specificity โ Video Summary NeuroImage 2022 | NeuroImage 2021 |
| ๐ 2023 and Earlier | ||
| Oct 19, 2022 | Various | Erwin Hahn Lecture โ Full Playlist |
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 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.
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”
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”
This page lists all open layer-fMRI job opportunities.
Suggestions are welcome to layerfMRI@gmail.com
In this blog post, I want to share my thoughts on the number of layers that should be extracted from any given dataset. I will try to give an overview of how many layers are usually extracted in the field, I’ll describe my personal choices of layer numbers, and I will try to discuss the challenges of layer signal extraction along the way.
Recently, my adviser Peter Bandettini asked me to compile a list of all potential applications for layer-fMRI. It was a fun exercise to think about it. Below, you find a list of all potential applications that I could think of.ย Continue reading “List of potential layer-fMRI application studies”
This post contains a collection of recently presented powerpoint slides.
There is a long list of software packages that are capable of performing high-resolution MRI analysis.
Some of them are used by multiple groups and some of them are customized for specific studies only.
In this post, I want to give an overview over the most important software packages, their advantages and disadvantages, and their popularity in the field.
There are about 80 people with a strong interest in layer-fMRI.
The whole list can be seen here.
These people are included in the listserv:ย laminar.imaging.network@gmail.com
To subscribe, please write an informal email to laminar.imaging.network@gmail.com
Currently there are more then 100 ultra-high field scanners installed.
An open google map of all scanners:
layer fMRI blog 