Author: renzohuber

Which sequence is best for layer-fMRI? A graphic story in cynical metaphors.

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.” →

Third Virtual Layer-fMRI โ€˜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. 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 โ€˜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 โ€œhackโ€ 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” →

layer-fMRI seminar

Layer-fMRI Research Seminar Series

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.

๐Ÿ“… Meeting Information

๐Ÿ“บ YouTube Playlist

๐Ÿ“‹ All Presentations

Complete list of all seminars, including past presentations. Click on speaker names or topics for links to full papers and recordings.

๐Ÿ“… Date๐ŸŽค Speaker๐Ÿ“ Topic
Dec 21, 2026โ€”Winter break โ€“ No Meeting
Dec 7, 2026Gordon SmithCommon principles underlying the development of large-scale cortical networks.
Nov 23, 2026
11 AM		Jingnan DuImaging cortical networks with precision
Nov 9, 2026Joseph EmersonOrientation-tuned surround suppression exhibits a unique laminar signature in the human primary visual cortex. ๐Ÿ“„ Paper
Oct 26, 2026ISMRM SubmittersAbstract feedback and discussion (deadline Oct 28)
Oct 12, 2026โ€”๐Ÿ–๏ธ Indigenous Peoples’ Day โ€“ No Meeting
Sept 28, 2026Johannes FranzCortical myeloarchitectural types in a 75 ฮผm isotropic whole human brain ex-vivo dataset
Sept 14, 2026Nadine GraedelHigh-Resolution BOLD fMRI at 7T in Regions of High Field Inhomogeneity
Aug 31, 2026Xin 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, 2026Antonia MassmannThe development of sensory processing in the human infant brain
Aug 3, 2026Saskia BollmannFirst impression of the Terra.X Impulse MRI scanner for precision neuroscience research
July 20, 2026โ€”โ˜€๏ธ Summer Break
July 6, 2026Tommy ClausnerFrequency and Laminar Profile of Feature Specific Activity Revealed by EEG-fMRI
June 22, 2026Daniel HaeneltRemoving the effect of macro-vascular veins from mesoscale fMRI
June 8, 2026Yuhui ChaiResolving mesoscale brainstem-prefrontal-striatal pathways underlying decisions upon salient events using submillimeter-resolution fMRI ๐Ÿ“บ
May 25, 2026โ€”๐Ÿ–๏ธ Holiday
May 11, 2026โ€”Canceled โ€“ ISMRM Conference
April 27, 2026Renzo, AllessandraISMRM Rehearsal Presentations
April 13, 2026Lasse KnudsenLatest progress of high-res fMRI at 10.5T
March 30, 2026Suvi HรคkkinenFunctional imaging of hippocampal layers using VASO on the Next Generation (NexGen) 7T
March 16, 2026Wietske van der ZwaagMesoscale (f)MRI of the Cerebellum
March 2, 2026โ€”Canceled by speaker
Feb 16, 2026โ€”Presidents’ Day โ€“ No Meeting
Feb 2, 2026Dana RamadanMacrovascular contributions to resting-state fMRI signals: A comparison between EPI and bSSFP at 9.4 Tesla
Jan 19, 2026โ€”Shifted by speaker request
๐Ÿ“Œ 2025 Events
Dec 8, 2025Saskia BollmannTowards Quantitative Analysis of Vascular Characteristics in the Human Brain
Nov 24, 2025Alejandro MonrealLayer-fMRI spirals: VASO fMRI spirals, 11.7T fMRI spirals, etc.
Nov 10, 2025Omer Faruk GulbanMeso-vessel imaging with 7 T MRI: Linking anatomy and function in living humans
Oct 27, 2025Renzo Huber
Divya Varadarajan
Alessandra Pizzuti		PNS Optimized Pulses for EPI (POPE): Simple adjustment to gradient pulse shape for practical high-resolution fMRI
SurfScribe: Cortical surfaceโ€“driven 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, 2025CMRR WorkshopHands-on Layer-fMRI Analysis Course โ€“ LayNii, FreeSurfer, BrainVoyager (Luca Vizioli, Renzo Huber, Jonathan Polimeni, Rainer Goebel)
Sept 29, 2025Shahin NasrMesoscale cortical plasticity in humans revealed by high-resolution functional MRI
Sept 15, 2025Amelia StromQuantification of cerebral cortical displacement driven by visual stimulation using motion-encoded stimulated-echo EPI at 7T
Sept 1, 2025โ€”Labor Day โ€“ No Meeting
Aug 18, 2025Sharif KronemerThe human brain mechanisms of afterimages: From networks to cortical layers
Aug 4, 2025Marianna SchmidtMesoscale functional connectivity within the human primary visual cortex
June/July 2025โ€”Summer Break
May 27, 2025Faruk GulbanFaster, Finer, Higher, Larger with LayNii IDA: Meso Veins Meet Layer fMRI
May 12, 2025โ€”Canceled โ€“ ISMRM Hawaii
April 28, 2025Stephanie, Khazar, Renzo, MarcoISMRM Mock Presentations โ€“ Dynamic CSF volume imaging, 3rd order shim, layer-fMRI in hippocampus, layer-toolbox
April 14, 2025Elisa ZamboniMapping Curvature Domains in Human V4 Using CBV-Sensitive Layer-fMRI at 3T
March 31, 2025โ€”Canceled โ€“ ISMRM Workshop Annapolis
March 17, 2025Gabi LohmannCylarim: A new tool for laminar-specific fMRI analysis
March 3, 2025Fraser AitkenLayer-fMRI and Epilepsy
Feb 17, 2025โ€”Presidents’ Day โ€“ No Meeting
Feb 3, 2025Renzo HuberUpdates on EPI Artifact Mitigations โ€“ Towards whole brain layer-fMRI with faster TRs
Jan 22, 2025
10:30 AM		Emma BrouwerCerebellar Imaging using 7T MRI
๐Ÿ“Œ 2024 Events
Dec 13, 2024Burak AkinLayer-fMRI Patch Analysis โ€“ Looking for instantaneous layer profiles
Nov 29, 2024Ethan BuchLayer-fMRI VASO on motor learning (Leo Cohen’s lab)
Nov 15, 2024โ€”Canceled โ€“ SFN Conference in DC
Nov 1, 2024Group DiscussionISMRM Abstract Submissions (10:30โ€“11:30 AM)
Oct 18, 2024Kenny ChungT1234 EPI โ€“ Discussion of ISMRM submissions (10:30โ€“11:30 AM)
Oct 4, 2024โ€”Canceled โ€“ Boston Workshop on Layer-fMRI
Sept 20, 2024GroupRehearsal Talks for Boston Layer-fMRI Workshop (10:30โ€“11:30 AM)
Sept 6, 2024Grant HartungCapillary Density Induces “Microvascular Biases” in Layer-fMRI BOLD โ€“ Insights from realistic vascular modeling
Aug 23, 2024โ€”Canceled โ€“ Summer Holidays
July 26, 2024JiajiaLayer-specific finger representations in human area 3b โ€“ OHBM abstract
June 28, 2024Silvina HorovitzHigh-resolution VASO in focal hand dystonia patients (30 min earlier)
June 14, 2024Renzo HuberISMRM Post-Discussion
May 31, 2024Renzo, YuhuiISMRM Rehearsal โ€“ Fuzzy Ripples talk and Recent Advances in Layer-fMRI, VAPER connectivity
May 17, 2024Daniel ZaldivarLayer-dependent changes of neural activity underlying laminar fMRI
May 3, 2024Faruk GulbanTutorial: ITK-SNAP Segmentation โ€“ Video
April 19, 2024TylerCortical-subcortical connection overview
April 5, 2024Sam Audrain, Andrew PersicettiCapturing layer-fMRI in inferior parts of the cortex
March 22, 2024Eli MeriamInformal discussion โ€“ Future layer-fMRI study on texture processing in V1/V2
March 8, 2024Aneurin KennerleyDIANA โ€“ Human line scanning at 3T
Feb 22, 2024Atena AkbariPhase-regression and VASO for layer-fMRI in ocular dominance columns
Feb 8, 2024Jun HuaLayer-fMRI with memory encoding in the entorhinal cortex
Jan 25, 2024Sohuyn HanSpin-Echo BOLD for Improved Layer-Specificity โ€“ Video Summary
NeuroImage 2022 | NeuroImage 2021
๐Ÿ“Œ 2023 and Earlier
Oct 19, 2022VariousErwin Hahn Lecture โ€“ Full Playlist

Baseline CBV and itโ€™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 itโ€™s role for the interpretation of layer-dependent VASO signals.” →

Second Virtual Layer-fMRI โ€˜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.

Continue reading “Second Virtual Layer-fMRI โ€˜Dinner’: Laminae in the brain; fMRI vs. electrophysiology” →

brain art

This is a collection of brain art that I made.

2023

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Bark

2020 Candy brain, generated with LAYNII’s LN2_COLUMNS from Faruk Omer Gulban


2020 challenge by OHBM

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2020: The Australians die equi-distant layers long before is was cool: Aboriginal art in LAYINII.

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2020: The brain as seen from a precessing proton.ezgif-6-ee5b65c8b37b.gif

2020: Feeling lost in the hunt for resolution. Nothing will ever be high enough

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2019: pulsed source

2019: Verzwirbelter Zwirn II

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2019: spectral brain

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2019: brain shape in in the style of a Cajal drawing of a Purkinje Cell

2018: broken phone screen edited with deep-learning algorithm

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2019: MRI fireworks with broccoli

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2018: Never ending layers

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2018: Joy of layering (based on idea from Erika Raven)

The profiles refer to myelin stain profiles of multiple brain areas. The thickest one it from motor cortex and the thinnest one is from sensory cortex. The y-axis refers to gray values of drawings from Theodor Kaehs.

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2018: The devils brain (3D print, painted with nail polish)

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2018: The horned brain

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2018: the exploding brain (when the cortical smoothing algorithm is buggy)

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2018: The firing brain

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2018: Physiological noise

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2018: You are your brain and your brain is us (Wax on plastic)

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2018: Layer T-shirt

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2018: growing layers

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2018: surfaces on volume

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2018 I am my brain and my brain is me

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2017 flow mapping in DC (the voxel state)

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2017 Weapon of choice

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2016 Fingerprinting

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2016 Fractal wax

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2017 Brain storming

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2017 Cajal

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2017 Weapon of choice and fractal brain tree

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2015: Bark

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2015: Brain roots

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2016: Origami

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2015: Zwirbelnder Zwirn

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2016: Brain ball (Franklin Institute gift shop)

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2016: HAWAII: Surfing the surfaces

surf_gif

2016: Aborigines: They did equi-distant long before it was cool

aboriginal

2015: paper

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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 โ€œassigning layers to cortical depthsโ€ (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.

Continue reading “Quality assurance measures for layer-fMRI time series: How to obtain them in LAYNII” →

Removing unwanted venous signal from GE-BOLD maps: Overview of vein removal models and implementations in LAYNII

Did you acquire your data with GE-BOLD EPI and now worry about draining vein contaminations?ย  There are several models out there for post-processing 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.

Continue reading “Removing unwanted venous signal from GE-BOLD maps: Overview of vein removal models and implementations in LAYNII” →

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

Continue reading “layer-fMRI Webinar MBIC 2020” →

Layer-fMRI Jobs

 

This page lists all open layer-fMRI job opportunities.

Suggestions are welcome to layerfMRI@gmail.com

Tweet intro
Don’t we all feel like Daniel in his Tweet(screenshot taken with permission)