I want to talk about something I have been working on, and want to be upfront that its agent assisted coding - basically, an opinionated toolbox for intensive ("hardcore") or layer fMRI projects - ones that demand precision: fastfuncstuff here: github.com/dowdlelt/fas...

GitHub - dowdlelt/fastfuncstuff: A repository of GPU accelerated fMRI tools based on AFNI, FSL and others along with fMRI simulation code. A bit a mess, but we are having fun.

A repository of GPU accelerated fMRI tools based on AFNI, FSL and others along with fMRI simulation code. A bit a mess, but we are having fun. - dowdlelt/fastfuncstuff

github.com

Dr. Tianye Zhai’s careful and exhaustive new paper evaluating the effects of numerous fMRI denoising pipeline components, alone and in combination, just came out in HBM - check it out! onlinelibrary.wiley.com/doi/10.1002/...

Benchmarking fMRI Denoising Pipelines

This paper benchmarked fMRI denoising pipelines on task- and resting-state, single- and multi-echo fMRI datasets, in a modern 1-step regression framework, with pre-whitening and time-shifted physiolo...

onlinelibrary.wiley.com

About to start my travel to #OHBM2026 Excited to help organize a full day ed course on multi-echo fMRI. Schedule is here: me-ica.github.io/ohbm-2026-mu... @enekourunuela.com @drjuliamoser.bsky.social @dowdlelt.bsky.social @ohbmofficial.bsky.social

If you are setting up the meso-veins protocol for the first time at your 7T (doi.org/10.1126/scia...), you should watch this video where I am providing the most up to date pointers. As well as the tips on quality controlling your images: youtu.be/57URvSjUYRY

How do we define "good" fMRI data? Especially with resting state, there are circularity risks if we evaluate data quality as showing the networks we expect to see. Javier Gonzalez-Castillo (& me & others) developed pBOLD, a new metric that uses multi-echo info. www.biorxiv.org/content/10.6... 1/8

New layer-fMRI manuscript finding laminar response differences across orientation-tuned surround suppression. doi.org/10.64898/202... By Emerson et al

14 months after submission, our article “Stimulus-modulated approach to steady state (SASS): a flexible paradigm for event-related fMRI" is now out in @natmethods.nature.com . You can read it here rdcu.be/ePJo6 It is the first first author paper from my student @renilmathew.bsky.social 👏🏽👏🏽👏🏽 …1/N

Stimulus-modulated approach to steady state (SASS): a flexible paradigm for event-related fMRI

Nature Methods - Stimulus-modulated approach to steady state (SASS) is an acquisition scheme for event-related fMRI that generates data with high temporal signal-to-noise ratios interspaced with...

rdcu.be

New AFNI Academy playlist! This tutorial presents afni_proc.py's quality control HTML for single subject FMRI. The APQC HTML has systematic views of data and useful derived quantities. Users can instantly rate, comment and query the fully processed subject data. www.youtube.com/watch?v=hD9z...

Data only shows associations. Turning those into claims about mechanism or causation? That requires a Rosetta Stone of prior knowledge + theory. Resting-state fMRI is purely observational; correlation is its currency. From this, plenty of "theoretical toys" about brain function can be built...

bioRxiv Neuroscience@biorxiv-neursci.bsky.social · 11mo ago

Resting-State fMRI and the Risk of Overinterpretation: Noise, Mechanisms, and a Missing Rosetta Stone https://www.biorxiv.org/content/10.1101/2025.09.16.676611v1

Nice work by @yoichimiyawaki.bsky.social showing the fMRI hemodynamic response contains enough info to decode stimulus type within 2sec. Happy to have helped with this project. www.biorxiv.org/content/10.1...

Rapid decoding of neural information representation from ultra-fast functional magnetic resonance imaging signals

High spatio-temporal resolution is crucial for neuroimaging techniques to improve our understanding of human brain function. While the fMRI signal is slow and shows a spread in latencies over space, t...

biorxiv.org

🚨Paper alert!🚨 TL;DR first: We used a pre-trained deep neural network to model fMRI data and to generate images predicted to elicit a large response for each many different parts of the brain. We aggregate these into an awesome interactive brain viewer: piecesofmind.psyc.unr.edu/activation_m...

#Neuroimaging crowd, hear me out! 👀 Did you ever want to add #EyeTracking to your #fMRI study but found it too much hassle? Got existing data you’d love to add eye tracking to? Consider trying out *MR-based eye tracking* (i.e. inferring gaze from eye voxels)! Here is a 🧵 with a few options!👇 1/9

A starter pack of layer-fMRI folks here: go.bsky.app/TUWFNzg

For all those researchers wanting to do hemodynamic deconvolution with my #neuroimaging pySPFM package: Just updated the documentation to include two clear examples of how to call the pySPFM package and what outputs you can expect. Should help you get the most out of this tool.

While fine-tuning 3D EPI parameters, we captured an impressively clear view of the human LGN! If you look closely, you can almost make out faint layers—wish they were more distinct though 🫤

New layer-fMRI review on the methodological challenges and prospects of laminar fMRI. By Yuhui Chai et al., doi.org/10.1093/psyr...

The craziest paper I have ever done is this thought experiment with Albert Gidon and Matt Larkum. In the first journal, reviewer 1 recommended that we should not try to publish this; reviewer 2 called it "wacky". Thanks for the motivation: A sequel is coming up! journals.plos.org/plosbiology/...

Does brain activity cause consciousness? A thought experiment

The authors of this Essay examine whether action potentials cause consciousness in a three-step thought experiment that assumes technology is advanced enough to fully manipulate our brains.

journals.plos.org

"A neural basis for distinguishing imagination from reality" This new preprint from @nadinedijkstra.bsky.social @peterkok.bsky.social & @smfleming.bsky.social is simply *stunning*. Beautifully elegant design, cognitive modelling, and brain imaging. Total package. osf.io/preprints/ps... 🧠📈 🧪

Friendly reminder for everyone who has just joined #neuroskyence : There is a #neuroimaging feed you can follow too! And publishing there is as easy as using the hashtag. Just like it and pin it 👇 bsky.app/profile/did:...