Matt Cieslak
@cieslakmatt.bsky.social
Director of Informatics at PennLINC. Diffusion MRI, open science, computation and statistics
After years of development and testing, we are happy to present our work in "Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications"! www.biorxiv.org/content/10.1.... A thread:
Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications
The landmark ongoing HEALthy Brain and Cognitive Development (HBCD) study will longitudinally chart brain development in a large sample (projected n=7,200) of infants through age 10 years with multimo...
www.biorxiv.org
November 11, 2025 at 10:03 PM
After years of development and testing, we are happy to present our work in "Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications"! www.biorxiv.org/content/10.1.... A thread:
Reposted by Matt Cieslak
Join us for the #NeuroHackademy Neuroimaging and Data Science networking event at this year's @sfn.org meeting. Tues. Nov. 18th from 7–9pm at the Marriott Marquis, Grand Ballroom 4. The event is free; food and drink will be available for purchase from the hotel.
October 20, 2025 at 7:41 PM
Join us for the #NeuroHackademy Neuroimaging and Data Science networking event at this year's @sfn.org meeting. Tues. Nov. 18th from 7–9pm at the Marriott Marquis, Grand Ballroom 4. The event is free; food and drink will be available for purchase from the hotel.
Reposted by Matt Cieslak
🚨 New science alert! Our cross-species study, now in Nature Neuroscience, demonstrates psychedelics distort how we should interpret functional brain imaging.
👇🧵
nature.com/articles/s41...
#Neuroscience #Psychedelics #BrainImaging
👇🧵
nature.com/articles/s41...
#Neuroscience #Psychedelics #BrainImaging
Psychedelic 5-HT2A receptor agonism alters neurovascular coupling and differentially affects neuronal and hemodynamic measures of brain function
Nature Neuroscience - Padawer-Curry et al. show that the hallucinogenic 5-HT2A receptor agonist DOI alters neurovascular coupling in mice, with implications for the interpretation of human fMRI...
nature.com
October 15, 2025 at 8:18 PM
🚨 New science alert! Our cross-species study, now in Nature Neuroscience, demonstrates psychedelics distort how we should interpret functional brain imaging.
👇🧵
nature.com/articles/s41...
#Neuroscience #Psychedelics #BrainImaging
👇🧵
nature.com/articles/s41...
#Neuroscience #Psychedelics #BrainImaging
Reposted by Matt Cieslak
Excited to share that our work introducing the Reproducible Brain Charts (RBC) data resource is now published in Neuron!! 🎉
📚 Read the paper: authors.elsevier.com/c/1lpaF3BtfH...
🧠 Explore the RBC dataset: reprobrainchart.github.io
📚 Read the paper: authors.elsevier.com/c/1lpaF3BtfH...
🧠 Explore the RBC dataset: reprobrainchart.github.io
(1/18) Now out on BioRxiv‼️ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health | doi.org/10.1101/2025...
Funded by National Institute of Mental Health (NIMH)
Funded by National Institute of Mental Health (NIMH)
Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health
Major mental disorders are increasingly understood as disorders of brain development. Large and heterogeneous samples are required to define generalizable links between brain development and psychopat...
doi.org
September 22, 2025 at 9:51 PM
Excited to share that our work introducing the Reproducible Brain Charts (RBC) data resource is now published in Neuron!! 🎉
📚 Read the paper: authors.elsevier.com/c/1lpaF3BtfH...
🧠 Explore the RBC dataset: reprobrainchart.github.io
📚 Read the paper: authors.elsevier.com/c/1lpaF3BtfH...
🧠 Explore the RBC dataset: reprobrainchart.github.io
Reposted by Matt Cieslak
New preprint from stellar IRTG PhD student Amelie Rauland + team on white matter bundle reconstruction! Shows that WM bundles can be reliably extracted from simple 32-direction dMRI & features predict cognition - huge potential for legacy and clinical data. Thread 👇
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
September 7, 2025 at 2:59 PM
New preprint from stellar IRTG PhD student Amelie Rauland + team on white matter bundle reconstruction! Shows that WM bundles can be reliably extracted from simple 32-direction dMRI & features predict cognition - huge potential for legacy and clinical data. Thread 👇
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Reposted by Matt Cieslak
New paper alert! This paper describes the work that we have been doing in the last few years to create a software ecosystem for tractometry that is extensible, interoperable, and generally useful.
New pub alert 📖
Our very own @arokem.org co-authored "A software ecosystem for brain tractometry processing, analysis, and insight" for PLoS Computational Biology.
journals.plos.org/ploscompbiol...
Our very own @arokem.org co-authored "A software ecosystem for brain tractometry processing, analysis, and insight" for PLoS Computational Biology.
journals.plos.org/ploscompbiol...
A software ecosystem for brain tractometry processing, analysis, and insight
Author summary The human brain is a highly inter-connected system. Information about the environment and about internal states is effectively distributed and integrated through neural pathways that ra...
journals.plos.org
August 20, 2025 at 5:22 PM
New paper alert! This paper describes the work that we have been doing in the last few years to create a software ecosystem for tractometry that is extensible, interoperable, and generally useful.
Reposted by Matt Cieslak
Looking for @theabcdstudy.bsky.social fMRI timeseries data?It's all in the 6.0 data release, thanks to @drdamienfair.bsky.social and team at ABCC 🧠: docs.abcdstudy.org/latest/docum...
ABCD-BIDS community collection
docs.abcdstudy.org
July 30, 2025 at 1:54 PM
Looking for @theabcdstudy.bsky.social fMRI timeseries data?It's all in the 6.0 data release, thanks to @drdamienfair.bsky.social and team at ABCC 🧠: docs.abcdstudy.org/latest/docum...
Reposted by Matt Cieslak
(1/4) Our recent work shows DTI-ALPS is confounded by white matter geometry (crossing fibers, undulation, dispersion), ALPS-asymmetry signature (ALPS measures asymmetry of diffusion) occurs throughout all WM, and ALPS-WM is not always orthogonal to PVS onlinelibrary.wiley.com/share/TPCABU...
July 27, 2025 at 1:06 PM
(1/4) Our recent work shows DTI-ALPS is confounded by white matter geometry (crossing fibers, undulation, dispersion), ALPS-asymmetry signature (ALPS measures asymmetry of diffusion) occurs throughout all WM, and ALPS-WM is not always orthogonal to PVS onlinelibrary.wiley.com/share/TPCABU...
SO COOL
How does the human brain coordinate hierarchical cortical development? Our work in Nature Neuroscience identifies a role for thalamocortical structural connectivity in the expression of hierarchical periods of cortical plasticity & environmental receptivity in youth 🧵 www.nature.com/articles/s41...
July 8, 2025 at 5:14 PM
SO COOL
Reposted by Matt Cieslak
Alert! ... for the child development world!
@fluxsociety.bsky.social @fitngin.bsky.social
The Healthy Brain and Child Development (HBCD) Study has released its first data wave - it’s massive.
Check here:
docs.hbcdstudy.org
and here:
nbdc-datahub.org
Here’s why it matters 🧠🍼
@fluxsociety.bsky.social @fitngin.bsky.social
The Healthy Brain and Child Development (HBCD) Study has released its first data wave - it’s massive.
Check here:
docs.hbcdstudy.org
and here:
nbdc-datahub.org
Here’s why it matters 🧠🍼
June 29, 2025 at 2:18 AM
Alert! ... for the child development world!
@fluxsociety.bsky.social @fitngin.bsky.social
The Healthy Brain and Child Development (HBCD) Study has released its first data wave - it’s massive.
Check here:
docs.hbcdstudy.org
and here:
nbdc-datahub.org
Here’s why it matters 🧠🍼
@fluxsociety.bsky.social @fitngin.bsky.social
The Healthy Brain and Child Development (HBCD) Study has released its first data wave - it’s massive.
Check here:
docs.hbcdstudy.org
and here:
nbdc-datahub.org
Here’s why it matters 🧠🍼
Reposted by Matt Cieslak
(1/18) Now out on BioRxiv‼️ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health | doi.org/10.1101/2025...
Funded by National Institute of Mental Health (NIMH)
Funded by National Institute of Mental Health (NIMH)
Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health
Major mental disorders are increasingly understood as disorders of brain development. Large and heterogeneous samples are required to define generalizable links between brain development and psychopat...
doi.org
February 27, 2025 at 8:57 PM
(1/18) Now out on BioRxiv‼️ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health | doi.org/10.1101/2025...
Funded by National Institute of Mental Health (NIMH)
Funded by National Institute of Mental Health (NIMH)
I'm a huge fan of this project
Amelie Rauland (all star via IRTG student w/ @sbe.bsky.social ) will be presenting "Benchmarking Reconstruction Methods for Bundle Segmentation in Single-Shell dMRI" on Friday and Saturday, Poster #1283
June 25, 2025 at 2:49 PM
I'm a huge fan of this project
Reposted by Matt Cieslak
@kevin-y-sun.bsky.social will be presenting his work on "Copy Number Variant Risk Scores Are Associated with Personalized Functional Brain Network Topography" Wed, June 25, 13:15 - 15:15 & Thus, June 26, 13:45 - 15:45
June 25, 2025 at 12:50 AM
@kevin-y-sun.bsky.social will be presenting his work on "Copy Number Variant Risk Scores Are Associated with Personalized Functional Brain Network Topography" Wed, June 25, 13:15 - 15:15 & Thus, June 26, 13:45 - 15:45
Reposted by Matt Cieslak
@audreycluo.bsky.social will be presenting her fab work on "Two Axes of White Matter Development" on Wed, June 25, 13:15 -15:15 & Thurs, June 26, 13:45 -15:45; Poster #1010.
June 25, 2025 at 12:49 AM
@audreycluo.bsky.social will be presenting her fab work on "Two Axes of White Matter Development" on Wed, June 25, 13:15 -15:15 & Thurs, June 26, 13:45 -15:45; Poster #1010.
Reposted by Matt Cieslak
@goliashf.bsky.social is ALSO presenting "Systematic dynamical profiling to discover and manipulate the dynamical regime of the primate brain" Thursday, Jun 26: 9:00 AM – 10:15 AM during the computational dynamics symposium in Room M2.
June 25, 2025 at 12:44 AM
@goliashf.bsky.social is ALSO presenting "Systematic dynamical profiling to discover and manipulate the dynamical regime of the primate brain" Thursday, Jun 26: 9:00 AM – 10:15 AM during the computational dynamics symposium in Room M2.
Reposted by Matt Cieslak
@goliashf.bsky.social is presenting (via video, 🥲) "Reproducible Brain Charts: An Open Data Resource for Mapping the Developing Brain and Mental Health" on Friday, Jun 27: 11:30 AM – 12:45 PM. This talk is part the Neuroinformatics and Data Sharing session in Room M3 (Mezzanine Level).
June 25, 2025 at 12:41 AM
@goliashf.bsky.social is presenting (via video, 🥲) "Reproducible Brain Charts: An Open Data Resource for Mapping the Developing Brain and Mental Health" on Friday, Jun 27: 11:30 AM – 12:45 PM. This talk is part the Neuroinformatics and Data Sharing session in Room M3 (Mezzanine Level).
Reposted by Matt Cieslak
@stevenmeisler.com is presenting "A quality-rated, analysis-ready release of 26,174 dMRI sessions from the ABCD Study" Friday / Saturday 1810. Wooo!!!!
June 25, 2025 at 12:39 AM
@stevenmeisler.com is presenting "A quality-rated, analysis-ready release of 26,174 dMRI sessions from the ABCD Study" Friday / Saturday 1810. Wooo!!!!
Reposted by Matt Cieslak
The Baller Lab is thrilled to announce that @elenaccooper.bsky.social just had her first first-author publication! “Investigating mood and cognition in people with multiple sclerosis: a prospective cross-sectional study protocol” is now published on BMJ Open: bmjopen.bmj.com/content/15/5/e094733! 🧠
Investigating mood and cognition in people with multiple sclerosis: a prospective cross-sectional study protocol
Introduction Multiple sclerosis (MS) is an immune-mediated neurological disorder that affects one million people in the USA. Up to 50% of patients with MS experience depression, yet the mechanisms of ...
bmjopen.bmj.com
June 3, 2025 at 8:09 PM
The Baller Lab is thrilled to announce that @elenaccooper.bsky.social just had her first first-author publication! “Investigating mood and cognition in people with multiple sclerosis: a prospective cross-sectional study protocol” is now published on BMJ Open: bmjopen.bmj.com/content/15/5/e094733! 🧠
Some very cool imaging sequences in this one
Dreaming of a dataset that tracks mood, sleep & activity to better understand affective instability (AI)…AND paired with advanced MRI? 🤯
Check out our new bioRxiv preprint for a 13–23 y/o community sample (n=10 and growing!) with multi-echo fMRI, EMA & actigraphy: www.biorxiv.org/content/10.1...
Check out our new bioRxiv preprint for a 13–23 y/o community sample (n=10 and growing!) with multi-echo fMRI, EMA & actigraphy: www.biorxiv.org/content/10.1...
May 6, 2025 at 3:46 PM
Some very cool imaging sequences in this one
We think of white matter as the brain's highways—uniform conduits between cortices. But what if we study development along tracts? Turns out the journey matters as much as the cortical destination! We're thrilled to share “Two Axes of White Matter Development” www.biorxiv.org/content/10.1...
1/n
1/n
March 20, 2025 at 5:19 PM
Reposted by Matt Cieslak
THRILLED to see this SI now out addressing the power and potential of focusing our lens on women. H/t to Tali for making space for these ideas to flourish and for a dream team of investigators to contribute!!
Advancing the science of women’s health | Science Advances www.science.org/doi/10.1126/...
Advancing the science of women’s health | Science Advances www.science.org/doi/10.1126/...
Advancing the science of women’s health
www.science.org
March 5, 2025 at 9:34 PM
THRILLED to see this SI now out addressing the power and potential of focusing our lens on women. H/t to Tali for making space for these ideas to flourish and for a dream team of investigators to contribute!!
Advancing the science of women’s health | Science Advances www.science.org/doi/10.1126/...
Advancing the science of women’s health | Science Advances www.science.org/doi/10.1126/...
Big update to CuBIDS! Now with even more precise descriptions of protocol variations in your BIDS data.
We're excited to announce version 1.2.0 of CuBIDS, a Python library for organizing BIDS datasets.
CuBIDS: Curation of BIDS — CuBIDS 1.2.0 documentation
cubids.readthedocs.io
February 28, 2025 at 6:24 PM
Big update to CuBIDS! Now with even more precise descriptions of protocol variations in your BIDS data.
I've been involved with this project since the very beginning and am very happy with how it ultimately turned out. The curation and processing was absolutely painstaking. Congratulations @goliashf.bsky.social on an excellent paper!!
(1/18) Now out on BioRxiv‼️ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health | doi.org/10.1101/2025...
Funded by National Institute of Mental Health (NIMH)
Funded by National Institute of Mental Health (NIMH)
Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health
Major mental disorders are increasingly understood as disorders of brain development. Large and heterogeneous samples are required to define generalizable links between brain development and psychopat...
doi.org
February 27, 2025 at 9:55 PM
I've been involved with this project since the very beginning and am very happy with how it ultimately turned out. The curation and processing was absolutely painstaking. Congratulations @goliashf.bsky.social on an excellent paper!!
Reposted by Matt Cieslak
Do you work on surface MRI such as HCP data? Our paper is finally out in Imaging Neuroscience, showing biases in surface fMRI. The revised ms has many new insights!
TLDR: Vertices are much closer to each other in sulci, resulting in (fake) high spatial autocorrelation. (1/5)
TLDR: Vertices are much closer to each other in sulci, resulting in (fake) high spatial autocorrelation. (1/5)
February 25, 2025 at 12:36 AM
Do you work on surface MRI such as HCP data? Our paper is finally out in Imaging Neuroscience, showing biases in surface fMRI. The revised ms has many new insights!
TLDR: Vertices are much closer to each other in sulci, resulting in (fake) high spatial autocorrelation. (1/5)
TLDR: Vertices are much closer to each other in sulci, resulting in (fake) high spatial autocorrelation. (1/5)
It's hard to overstate what a big deal this paper is: onlinelibrary.wiley.com/doi/10.1002/.... Head motion in dMRI is NOT like head motion in BOLD.
Head Motion in Diffusion Magnetic Resonance Imaging: Quantification, Mitigation, and Structural Associations in Large, Cross‐Sectional Datasets Across the Lifespan
We characterized motion during diffusion MRI scans across 16,995 image sessions and find that (1) modern preprocessing pipelines effectively mitigate motion to the point where biases are not detectab....
onlinelibrary.wiley.com
February 13, 2025 at 5:42 PM
It's hard to overstate what a big deal this paper is: onlinelibrary.wiley.com/doi/10.1002/.... Head motion in dMRI is NOT like head motion in BOLD.