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PennLINC

@pennlinc.bsky.social
230 followers 36 following 29 posts

The Lifespan Informatics and Neuroimaging Center at the University of Pennylvannia, headed by @ted-satterthwaite.bsky.social. This account is mostly for announcing new papers, lab members, etc.

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Steven Meisler @stevenmeisler.com · 14/10/2026
Excited that this paper, "Highly replicable multisite patterns of adolescent white matter maturation", has now been published in Neuron! It may be found at cell.com/neuron/fullt.... To freely access the paper for the next 50 days, please use this link: authors.elsevier.com/c/1nxdd3BtfH...
cell.com
Highly replicable multisite patterns of adolescent white matter maturation
Meisler et al. present a large public resource of fully processed diffusion MRI from the ABCD study and show that advanced diffusion measures and longitudinal harmonization improve the replicability a...
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 02/10/2026
Check out our new fully processed test retest open data resource on myelin-sensitive imaging! Huge congrats to the amazing @stevenmeisler.com and @tsalo.bsky.social + a superb team.
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Steven Meisler @stevenmeisler.com · 01/10/2026
There are many MRI approaches for studying myelin. But which ones are reliable, how do they relate to each other, and how do they behave in gray vs white matter? In our new preprint, we introduce Myelin Imaging Reliability and ReprOducibility Resource (MIRROR) 🧠🪞 📄🔗 www.biorxiv.org/content/10.6...
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Golia Shafiei @goliashf.bsky.social · 30/09/2026
So excited that our work is now published in PLOS Biology!! 🎉 Check out the final version here: doi.org/10.1371/jour... And for a bit more context and what we found, here’s our earlier thread: bsky.app/profile/goli...
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PennLINC @pennlinc.bsky.social · 30/09/2026
The new image is available on DockerHub. If you run into any problems or have suggestions please open an issue!
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PennLINC @pennlinc.bsky.social · 30/09/2026
New documentation is available at qsiprep.readthedocs.io/en/26.1.0rc1/ with a guide to upgrading to the new version at qsiprep.readthedocs.io/en/26.1.0rc1....
qsiprep.readthedocs.io
QSIPrep: Preprocessing of Diffusion MRI (q-space) Images — qsiprep 26.1.0rc1 documentation
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PennLINC @pennlinc.bsky.social · 30/09/2026
And: - Simplification of commandline arguments and more options for ignoring or forcing steps
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PennLINC @pennlinc.bsky.social · 30/09/2026
Also: - GPU acceleration / toggling options for TORTOISE, Synb0, Synthstrip / Synthseg, eddy - QSIPlan: see how input data will be grouped (including "virtual acquisitions") before running QSIPrep. - Gradient nonlinearity distortion correction using coef files or pre-computed displacement maps
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PennLINC @pennlinc.bsky.social · 30/09/2026
Major new features include: - Inclusion of TORTOISEv4 head motion / eddy current correction - Synb0-generated fieldmapless distortion correction reference - T2wreg from TORTOISEv4 for fieldmapless distortion correction - Hybrid fieldmap/registration-based susceptibility distortion correction
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PennLINC @pennlinc.bsky.social · 30/09/2026
We’ve been working on a major update to QSIPrep and are excited to announce that a release candidate is available for testing: version 26.1.0rc1.
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Valerie Jill Sydnor @valeriejsydnor.bsky.social · 02/09/2026
I am oh so happy to share that my K99/R00 "Linking Adolescent Environmental Enrichment to Association Cortex Plasticity and Psychiatric Resiliency" was awarded by the NIMH! And with that, I am on the job market! I can't wait to find the home of my future lab.
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Joëlle Bagautdinova @joelleba.bsky.social · 01/09/2026
Thrilled to share that this work is now published in Nature Human Behavior!!! 🥳🎉 doi.org/10.1038/s415...
doi.org
Anatomical white matter tracts span the cortical hierarchy to support cognitive diversity - Nature Human Behaviour
Bagautdinova et al. study how white matter tracts are organized along the brain’s hierarchy and how they connect diverse biological environments to support complex human cognition and neurodevelopment.
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Brooke Sevchik @bsevchik.bsky.social · 20/08/2026
Very excited to announce that this work is now published in Scientific Data! doi.org/10.1038/s415...
doi.org
A longitudinal data resource to study brain development and transdiagnostic variation in executive function - Scientific Data
Scientific Data - A longitudinal data resource to study brain development and transdiagnostic variation in executive function
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Marc Jaskir @marcjaskir.bsky.social · 18/08/2026
Many dMRI statistics have been investigated, but their whole-brain relationships are unclear. This makes it challenging to determine which statistics capture overlapping vs. unique microstructural information
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PennLINC @pennlinc.bsky.social · 07/07/2026
Huge thanks to the coauthors: @tsalo.bsky.social, @parkersingleton.bsky.social, @coreyhorien.bsky.social, @cieslakmatt.bsky.social, @lizzieflook.bsky.social, Sage Rush, @bsevchik.bsky.social, @tientong.bsky.social, Manuel Taso, @mdtisdall.bsky.social, David Roalf, @ted-satterthwaite.bsky.social /end
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PennLINC @pennlinc.bsky.social · 07/07/2026
Full derivatives are included too: MRIQC, fMRIPrep, tedana, and XCP-D outputs on OpenNeuro, plus Nilearn outputs on NeuroVault. 5/
openneuro.org
OpenNeuro
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PennLINC @pennlinc.bsky.social · 07/07/2026
Why phase data matters: it's almost never shared in fMRI studies, but it opens the door to better thermal noise removal, phase-based confound extraction, phase regression, complex ICA, and complex-valued modeling — none of which are standard in pipelines like fMRIPrep yet. 4/
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PennLINC @pennlinc.bsky.social · 07/07/2026
The extras that make this dataset unusual: – magnitude AND phase reconstruction – noRF ("noise-only") volumes – multiple field map types in both phase-encoding directions 3/
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PennLINC @pennlinc.bsky.social · 07/07/2026
What's in it: 8 young adults, scanned twice each. Per session — a T1 anatomical, 4 resting-state scans (2 single-echo, 2 complex multi-echo), and a multi-echo n-back working memory task. 2/
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PennLINC @pennlinc.bsky.social · 07/07/2026
New dataset out in Data in Brief 🧠 We're releasing an open, test-retest neuroimaging dataset built for directly comparing single-echo vs. multi-echo fMRI, head-to-head, in the same people. 1/
sciencedirect.com
A single-echo/multi-echo BOLD fMRI test-retest dataset
Functional MRI (fMRI) remains one of the primary tools for non-invasive studies of brain activity and organization in humans. Recently, multi-echo ima…
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Sheila Shanmugan @sheilashanmugan.bsky.social · 11/06/2026
We are currently recruiting a data analyst and a postdoctoral fellow to lead projects related to perinatal neuroimaging and reproductive psychiatry. Apply at the links below!
static.klipy.com
DGS: Apply Now & Register
ALT: DGS: Apply Now & Register
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Russ Poldrack @russpoldrack.org · 14/06/2026
Congrats to our own @markiewicz.bsky.social for winning the OHBM Open Science Award!
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 21/05/2026
Postdoc opening w/ a great team inc close collab Dan Wolf! fMRI + computational modeling in NIH-funded clinical high risk for psychosis study. U. Maryland in collaboration with UPenn + Mt. Sinai. Full posting here: umb.taleo.net/careersection/jobdetail.ftl?job=260000DJ
umb.taleo.net
Post-Doctoral Fellow
Click the link provided to see the complete job description.
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Steven Meisler @stevenmeisler.com · 19/04/2026
Given these scanner differences, harmonization is essential! In unharmonized data, acquisition batch explained up to 70% of microstructural variance. We used cutting-edge longitudinal nonlinear harmonization, which eliminated these effects while preserving developmental effects.
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Steven Meisler @stevenmeisler.com · 19/04/2026
Huge thanks to the incredible team of 50 co-authors who made this possible! Special thanks to our lab replicator + dMRI guru @cieslakmatt.bsky.social, the UMN team led by @drdamienfair.bsky.social, and my incredibly supportive postdoc advisor @ted-satterthwaite.bsky.social! Preprint: bit.ly/3QMLG0K
biorxiv.org
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BIDS (Brain Imaging Data Structure) @bidsstandard.bsky.social · 20/04/2026
We are pleased to announce that BIDS Extension Proposal 32 - Microelectrode Electrophysiology is open for community review! github.com/bids-standar... The review period is open from April 20 - May 1. #bids #neuroimaging #electrophysiology
github.com
Community Review: BEP032 - Microelectrode Electrophysiology · bids-standard bids-specification · Discussion #2406
We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 032! BEP032 extends the BIDS standard to describe microelectrode electrophysiology data. The draft specifica...
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BIDS (Brain Imaging Data Structure) @bidsstandard.bsky.social · 20/04/2026
We are pleased to announce that BIDS Extension Proposal 28 - Provenance is open for community review! github.com/bids-standar... The review period is open from April 20 - May 1. #bids #neuroimaging #provenance
github.com
Community Review: BEP028 - Provenance · bids-standard bids-specification · Discussion #2405
We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 028! BEP028 extends the BIDS standard to describe the provenance of BIDS datasets. It introduces new organiz...
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 19/04/2026
Huzzah for @stevenmeisler.com, whose preprint on our new fully-processed ABCD dMRI data resource is now out. The super-clear results from this monumental effort will undoubtably change the way we approach studies of white matter development going forward.
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Steven Meisler @stevenmeisler.com · 19/04/2026
Diffusion MRI (dMRI) is a powerful tool to study white matter maturation. In our new preprint, we process and distribute a new resource of >24,000 ABCD dMRI scans using open source tools! We then evaluate how methods shape inferences about development. 🔗 www.biorxiv.org/content/10.6...
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Golia Shafiei @goliashf.bsky.social · 14/04/2026
✨Excited to share that our new preprint, "Mapping developmental patterns of intrinsic timescale", is now available on bioRxiv!! 📚 doi.org/10.64898/202...
doi.org
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 14/04/2026
The PMADS Project: A Longitudinal Multimodal Cohort Study to Understand Risk for Perinatal Mood and Anxiety Disorders www.biorxiv.org/content/10.64898/20…
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Neurosynth @neurosynth.bsky.social · 10/02/2026
A systematic meta-analysis is hard work—and curation is often the hardest part. Y'all know this better than anyone, and we want to make it easier. What’s one specific piece of information you consistently had to find or extract from every paper? Tell us about it: tally.so/r/QKVbQG #neuroscience
media.tenor.com
a man is standing in a kitchen with his hands on his chest and asking for help .
Alt: Tom Cruise is standing in a kitchen with his hands on his chest and asking for help, saying "Help me, Help you"
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 05/01/2026
Refreshing this -- we are still reviewing applications for a spring/summer 2026 start date!!!
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Baller Lab @ballerlab.bsky.social · 03/12/2025
Excited to share that our new review, "Depression as a disease of white matter network disruption: Learning from Multiple Sclerosis," is out now in Biological Psychiatry! We propose MS as a powerful model for studying how white matter network changes contribute to depression.
biologicalpsychiatryjournal.com
Depression as a disease of white matter network disruption: Learning from Multiple Sclerosis
Depression is a common and debilitating psychiatric disorder that is associated with substantial morbidity and mortality. For nearly 40 years, scientists have attempted to localize depression in the b...
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 16/11/2025
BEYOND delighted to see two brilliant #PennLINC alumni -- @valeriejsydnor.bsky.social + @lindenmp.bsky.social -- named by The Transmitter as "Rising Stars of Neuroscience 2025". Super well deserved -- CONGRATS!!! www.thetransmitter.org/early-career...
thetransmitter.org
The Transmitter’s Rising Stars of Neuroscience 2025
We recognize the outstanding achievements of 25 neuroscientists who stand to shape the field for years to come.
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Brooke Sevchik @bsevchik.bsky.social · 12/11/2025
🧠I am excited to announce that our manuscript introducing a new data resource – PennLEAD (Penn Longitudinal Executive functioning in Adolescent Development) – is now available on bioRxiv. Below are some details highlighting our data resource🧵funded by NIMH R01MH113550 www.biorxiv.org/content/10.1...
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 12/11/2025
An Open, Fully-processed, Longitudinal Data Resource to Study Brain Development and Transdiagnostic Executive Function www.biorxiv.org/content/10.1101/202…
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Valerie Jill Sydnor @valeriejsydnor.bsky.social · 11/11/2025
Happy to share our review "Investigating hierarchical critical periods in human neurodevelopment” in @npp-journal.bsky.social! We examine neurobiological, environmental & behavioral evidence for human critical periods in sensory and association cortex +discuss new research directions rdcu.be/eMkVU 🧵
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 12/11/2025
Truly heroic work by the stellar @cieslakmatt.bsky.social + the HBCD dMRI working group team. Refactored QSIPrep + QSIRecon is the result of nearly 3y of concerted development + testing. It will be a total workhorse for HBCD -- and almost any other dMRI scan. Check it out for your data!!!
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Matt Cieslak @cieslakmatt.bsky.social · 11/11/2025
QSIPrep and QSIRecon are usable beyond HBCD. Code, containers, and documentation are openly available. github.com/PennLINC/qsi..., github.com/PennLINC/qsi...
github.com
GitHub - PennLINC/qsiprep: Preprocessing of diffusion MRI
Preprocessing of diffusion MRI. Contribute to PennLINC/qsiprep development by creating an account on GitHub.
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Matt Cieslak @cieslakmatt.bsky.social · 11/11/2025
We made numerous updates to the QSIPrep and QSIRecon software packages to better perform on HBCD’s infant/pediatric diffusion MRI. New preprocessing includes partial-Fourier Gibbs unringing, MP-PCA, 2-stage susceptibility distortion correction, SynthStrip/Synthseg and MNIInfant atlases.
A flow diagram describes the preprocessing workflow and additions specifically added for HBCD. Critical additions are Gibbs Unringing, a second stage of distortion correction, MNI Infant support and Synthstrip and Synthseg.
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Matt Cieslak @cieslakmatt.bsky.social · 11/11/2025
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:
biorxiv.org
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...
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Jonah Padawer-Curry, PhD @jonahpadawercurry.bsky.social · 15/10/2025
🚨 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
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...
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BIDS (Brain Imaging Data Structure) @bidsstandard.bsky.social · 29/09/2025
We are pleased to announce that BIDS Extension Proposal 20 - Eye Tracking is open for community review! github.com/bids-standar... The review period is open from September 29 - October 10. #bids #neuroimaging #eyetracking
github.com
Community Review: BEP020 - Eye Tracking · bids-standard bids-specification · Discussion #2218
We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 020! BEP020 extends the BIDS standard to formally specify eye-tracking recordings, which has previously been...
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BIDS (Brain Imaging Data Structure) @bidsstandard.bsky.social · 29/09/2025
We are pleased to announce that BIDS Extension Proposal 42 - Electromyogrpahy is open for community review! github.com/bids-standar... The review period is open from September 29 - October 10. #bids #neuroimaging #electromyography #emg
github.com
Community Review: BEP042 - Electromyography (EMG) · bids-standard bids-specification · Discussion #2219
We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 042! BEP042 extends the BIDS standard to include electromyography recordings. The draft specification may be...
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Valerie Jill Sydnor @valeriejsydnor.bsky.social · 08/07/2025
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...
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 08/07/2025
Check out this stellar work from the one-and-only @valeriejsydnor.bsky.social w/ team at @pennlinc.bsky.social + (many!) friends -- providing new evidence that thalamo-cortical connectivity coordinates the hierarchical progression of cortical plasticity in development. Out in @natneuro.nature.com.
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 25/06/2025
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
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 25/06/2025
@bencephalon.bsky.social from @aarona-b.bsky.social 's lab will be presenting "Integrating clinical and research imaging to uncover neuroanatomic deviations in 22q11.2 deletions" Wed, June 25, 13:15 -15:15 & Thurs, June 26, 13:45 -15:45; Poster #697
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Ted Satterthwaite @ted-satterthwaite.bsky.social · 25/06/2025
@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
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