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: Ömer Faruk Gülban, 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 μl) 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 μl) (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 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 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. 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.”| Date | Speaker | topic |
| April 13th 2026 | ||
| March 30th 2026 | Suvi Häkkinen | Functional imaging of hippocampal layers using VASO on the Next Generation (NexGen) 7T |
| March 16th 2026 | Wietske van der Zwaag | Mesoscale (f)MRI of the Cerebellum |
| March 2nd 2026 | Alard Roebroeck | Imaging layer specific meso- and microstructure in the human brain with ex vivo MRI and light sheet microscopy |
| Feb 16th 2026 | Holiday (Presidents Day) | |
| Feb 2nd 2026 | Dana Ramadan | Macrovascular contributions to resting-state fMRI signals: A comparison between EPI and bSSFP at 9.4 Tesla |
| Jan 19th 2026 | Tony Carricarte | Layer-specific spatiotemporal dynamics of feedforward and feedback in human visual object perception |
| Christmas break | ||
| Dec 8th 2025 | Saskia Bollmann | Towards Quantitative Analysis of Vascular Characteristics in the Human Brain |
| Nov 24th 2025 | Alejandro Monreal | layer-fMRI spirals: VASO fMRI spirals, 11.7T fMRI spirals, etc. |
| Nov 10th 2025 | Omer Faruk Gulban | Meso-vessel imaging with 7 T MRI: Linking anatomy and function in living humans |
| Oct 27th 2025 | Renzo Huber: PNS Optimized Pulses for EPI (POPE): Simple adjustment to gradient pulse shape for practical high-resolution fMRI. https://layerfmri.page.link/POPE Divya Varadarajan: SurfScribe: Cortical surface–driven automated online slice prescription applied to ultra-high-resolution vascular MRI Renzo Huber: LN2_FRISGO: A software solution for artifact mitigation in fast high-resolution fMRI. https://layerfmri.page.link/LN2_FRISGO Alessandra Pizzuti: Layer-fmri at 0.4 mm isotropic meets vascular mapping (0.35 mm iso): Partners or Confounders? | |
| Oct 13th 2025 | CMRR workshop | Hands on layer-fMRI analysis course with LayNii, FreeSurfer, and BrainVoyager. By Luca Vizioli, Renzo Huber, Jonathan Polimeni, Rainer Goebel. |
| Sept 29th 2025 | Shahin Nasr | Mesoscale cortical plasticity in humans revealed by high-resolution functional MRI |
| Sept 15th 2025 | Amelia Strom | Quantification of cerebral cortical displacement driven by visual stimulation using motion-encoded stimulated-echo EPI at 7T |
| Sept 1st 2025 | Labor Day | NO MEETING |
| Aug 18th 2025 | Sharif Kronemer | The human brain mechanisms of afterimages: From networks to cortical layers |
| Aug 4th 2025 | Marianna Schmidt | Mesoscale functional connectivity within the human primary visual cortex |
| June/July | summer break | NO MEETING |
| May 27th | Faruk Gulban | Faster, Finer, Higher, Larger with LayNii IDA: Meso Veins Meet Layer fMRI in High-Speed Data Exploration for the New Mesoscopic Era |
| May 12th | canceled | ISMRM Hawaii |
| April 28th | Stephanie, Khazar, Renzo, Marco | ISMRM mock presentations: dynamic CSF volume imaging, 3rd order shim, layer-fMRI in hippocampus, layer-toolbox |
| April 14th | Elisa Zamboni | Mapping Curvature Domains in Human V4 Using CBV-Sensitive Layer-fMRI at 3T |
| March 31st | canceled | ISMRM workshop Annapolis |
| March 17th | Gabi Lohmann | Cylarim: a new tool for laminar-specific fMRI analysis |
| March 3rd | Fraser Aitken | layer-fMRI and epilepsy |
| Feb 17th | canceled | Holiday (Washingtons birthday) |
| Feb 3rd | Renzo Huber | Updates on EPI artifact mitigations: towards whole brain layer-fMRI with faster TRs |
| Jan 22nd 10:30am | Emma Brouwer | Cerebellar imaging using 7T MRI |
| Winter break | ||
| Nov 27th | Lonike Faes | layer-fMRI in Auditory cortex: VASO sequence, NORDIC denoising, odd-ball tasks |
| Nov 13th | Khazar Ahmadi | Deep dive into hippocampus from a laminar perspective |
| Oct 30th | ISMRM abstracts | |
| Oct 16th | Grace Edwards | layer-fMRI language effects in V1 |
| Oct 2nd | Yuhui Chai | Blood-nulling versus tissue-suppression: Enhancing integrated VASO and perfusion (VAPER) contrast for laminar fMRI |
| Sept 18th | Tyler Morgan | Investigating neural responses using fast, non-selective MRI |
| Sept 4th | Daniel Haenelt | Understanding biases in functional magnetic resonance imaging |
| Aug 21st | Praveen Valsala | Accelerating bSSFP-fMRI with Spiral Readouts |
| Aug 7th | Renzo, Joelle, Tyler | 7TANA highlights |
| July 31st | Renzo Huber | 7T initiatives across sites |
| July 25th Thursday | Yulia Lazarova | |
| July 22th Monday | Alessandra Pizzuti | |
| July 10th | OHBM debriefing | Renzo on holidays |
| Jun 26th | OHBM | canceled |
| June 12th | Faruk Gulban | Phase Jolt fMRI |
| May 29th | Sebastian Dresbach | Laminar CBV and BOLD response-characteristics over space and time in human primary somatosensory cortex at 7T |
| May 15th | ISMRM post discusion | |
| May 1st, 2024 B1D55 | ISMRM mock presentations | Burak (Layer-ReHo), Renzo (lower brain structures) |
| April 31st 2024 virtual | ISMRM mock presentations | Tyler: DIANA & VAPER |
| April 17th, 2024 B1D55 | ISMRM preparations | Kenny (T1234), Lasse (NORDIC) |
| April 3rd, 2024 B1D55 | ISMRM mock presentations | Renzo (Motion symposium) |
| March 20th, 2024 B1D55 | Alessandra Pizzuti, about motion quartet | confirmed |
| March 6th, 2024 B1D55 | Marco Barilari: Characterizing multisensory integration and cross-modal plasticity in the cortex layers using VASO at high-res (7T) | hybrid |
| Feb 21st,2024, | Yuhui Chai | Improving laminar fMRI specificity by reducing macrovascular bias revealed by respiration effects |
| Feb 7th, 2024 virtual | Dongho Kim on Attention effects in human S1 | DIFFERENT TIME: 9:30am, virtual only |
| Jan 24th, 2024, virtual | SE-BOLD GE-BOLD, Face perception in V1 and ventral | Luca Vizioli, virtual only |
| Dec 27th | canceled | Christmas break |
| Dec 13th | Burak Akin | layer-fMRI patch analysis to look for instantaneous layer profiles |
| Nov 29th | Ethan Buch:layer-fMRI VASO on motor learning (Leo Cohen’s lab) | layer-fMRI VASO on motor learning (Leo Cohen’s lab) |
| Nov 15th | Canceled | due to SFN in DC |
| Nov 1st | ISMRM abstracts | 10:30-11:30 |
| Oct 18th | Kenny Chung: T1234 EPI. | Discussions of what we will submit on Nov 8th.10:30-11:30 |
| Oct 4th | Canceled | Canceled due to Boston Workshop : https://education.martinos.org/workshop-on-laminar-fmri/ |
| Sept 20th | Rehearsal talks for layer-FMRI talks in Boston | 10:30-11:30 |
| Sept 6th | Grant HartungVAN layers | Title: Capillary density induces “microvascular biases” in layer-fMRI BOLD: insights from realistic vascular modeling |
| Aug 23rd | Canceled due to holidays | |
| Aug 9th | OHBM debriefing? | |
| July 26th | Canceled due to OHBM | |
| July 12th | Jiajia presents | Layer-specific finger representations in human area 3b, abstract. |
| June 28th | high -resolution VASO in focal hand dystonia patients | Silvina HorovitzNote that this meeting will be 30 min earlier. |
| June 14th | ISMRM post discussion | Renzo Huber |
| May 31st | ISMRM rehearsal presentations | Renzo will present 9 min talk on fuzzy ripples and 20 min educational lecture on recent advances in the field of layer-fmri. Yuhui presented the VAPER connectivity. |
| May 17th | Daniel Zaldivar | Layer dependent changes of neural activity underlying laminar fMRI |
| May 3rd | Faruk | Tutorial on ITK snap segmentation, QnATo video https://youtu.be/tIuKG3rtVk4 |
| April 19th | Tyler | Cortical-subcortical connection overview |
| April 5th | Sam Audrain and Andrew Persicetti | Talking about their endeavors to capture layer-fMRI in some of the most inferior parts of the cortex. |
| March 22nd | Eli Meriam | Informal discussion of future layer fMRI study on texture processing in V1/V2 |
| March 8th | DIANA with Aneurin Kennerley | Tyler and Renzo are considering inviting Aneurin Kennerley to present his results with human line scanning at 3T. Aneurin confirmed |
| Feb 22nd | Atena Akbari | phase-regression and VASO for layer-fMRI in ocular dominance columns |
| Feb 8th | Jun Hua | Jun Hua will present his work on layer-fMRI with memory encoding in the entorhinal cortex. |
| Jan 25th 2023 | Sohuyn Han’s papers on Spin echo | Han S, Eun S, Cho H, Uludaǧ K, Kim SG. Improved laminar specificity and sensitivity by combining SE and GE BOLD signals. NeuroImage. 2022 www.doi.org/10.1016/j.neuroimage.2022.119675 Mini talk summary: https://youtu.be/ebDwcmcP4hw Han SH, Eun S, Cho HJ, Uludaǧ K, Kim SG. Improvement of sensitivity and specificity for laminar BOLD fMRI with double spin-echo EPI in humans at 7 T. NeuroImage. 2021 https://doi.org/10.1016/j.neuroimage.2021.118435 |
| Jan 11th 2023 | Canceled | Canceled |
| Dec 28th 2022 | Probably canceled with people on holidays? | |
| Dec 14th 2022 | One week before the OHBM deadline.Discussion of abstracts to be submitted | |
| Nov 30th 2022 | Yuhui presents connectivity results | Layer-specific functional connectivity with 3D VAPER fMRI http://submissions.mirasmart.com/ISMRM2023/ViewSubmissionPublic.aspx?sei=4oW3ybRR7 |
| Nov 2nd 2022 | canceled | |
| October 19th 2022 | Erwin Hahn Lecture | https://youtube.com/playlist?list=PLuA0pYRPZ4uAvC2uIHggzyQHveRrHLosx |
This page gives an overview of the bi-weekly meetings of layer-fMRI researchers at NIH/Maastricht/MGH and and friends. We meet every other week on Monday 10:00am (EST).
Email reminders are sent via the listserv: layer-fmri@researchlist.partners.org. You can subscribe by sending an email to subscribe-layer_fmri@researchlist.partners.org or contact me, and I can add you to the list.
We use this conference channel: https://mgb-org.zoom.us/my/layerfmri.
Some presentations are recorded. The Youtube channel of all recordings is here and embedded below (select video out of playlist with he button on the top right).
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. 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: 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 