Our latest PP led by @kanepav.bsky.social looking at how rsfMRI denoising affects data quality and BWAS effect sizes
New pre-print from @alexfornito.bsky.social, James Pang, and myself, looking at the effects of rs-fMRI pre-processing pipelines on FC quality and behavioural predictions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The efficacy of resting-state fMRI denoising pipelines for motion correction and behavioural prediction.
Resting state functional magnetic resonance imaging (rsfMRI) is a pivotal tool for mapping the functional organization of the brain and its relation to individual differences in behaviour. One challen...
www.biorxiv.org
December 4, 2024 at 1:32 AM
Our latest PP led by @kanepav.bsky.social looking at how rsfMRI denoising affects data quality and BWAS effect sizes
In-scanner thoughts contribute to resting-state functional connectivity pubmed.ncbi.nlm.nih.gov/42365014/ I've long thought that this is the "elephant in the room" of resting state #fMRI esp. for comparing groups. If two groups think & feel differently in the scanner, of course rsfMRI will differ!
June 28, 2026 at 1:46 PM
In-scanner thoughts contribute to resting-state functional connectivity pubmed.ncbi.nlm.nih.gov/42365014/ I've long thought that this is the "elephant in the room" of resting state #fMRI esp. for comparing groups. If two groups think & feel differently in the scanner, of course rsfMRI will differ!
Uncovering Hidden Brain Signals
By Neuroscience News
Source: Penn State University
neurosciencenews.com/rsfmri-brain...
♦️ rsfMRI measures brain activity by tracking blood flow changes but may miss “invisible” neural signals.
#neuroscience #brain #rsfMRI #fMRI #neuralsignals
By Neuroscience News
Source: Penn State University
neurosciencenews.com/rsfmri-brain...
♦️ rsfMRI measures brain activity by tracking blood flow changes but may miss “invisible” neural signals.
#neuroscience #brain #rsfMRI #fMRI #neuralsignals
Uncovering Hidden Brain Signals - Neuroscience News
A recent study offers new insights into how brain regions coordinate during rest, using resting-state fMRI (rsfMRI) and neural recordings in mice.
neurosciencenews.com
November 13, 2024 at 1:56 AM
Uncovering Hidden Brain Signals
By Neuroscience News
Source: Penn State University
neurosciencenews.com/rsfmri-brain...
♦️ rsfMRI measures brain activity by tracking blood flow changes but may miss “invisible” neural signals.
#neuroscience #brain #rsfMRI #fMRI #neuralsignals
By Neuroscience News
Source: Penn State University
neurosciencenews.com/rsfmri-brain...
♦️ rsfMRI measures brain activity by tracking blood flow changes but may miss “invisible” neural signals.
#neuroscience #brain #rsfMRI #fMRI #neuralsignals
In this new paper: shorturl.at/NbNLN, Zhang et al., combined rsfMRI, bulk and single cell gene expression data and found distinctive cellular fingerprints at the poles of the sensory-association rsfMRI gradient. But....
November 21, 2024 at 6:13 PM
In this new paper: shorturl.at/NbNLN, Zhang et al., combined rsfMRI, bulk and single cell gene expression data and found distinctive cellular fingerprints at the poles of the sensory-association rsfMRI gradient. But....
Characterizing variability in resting-state functional magnetic resonance imaging (rsfMRI) metrics: a normative modeling framework https://www.biorxiv.org/content/10.64898/2026.05.28.728381v1
June 1, 2026 at 8:16 PM
Characterizing variability in resting-state functional magnetic resonance imaging (rsfMRI) metrics: a normative modeling framework https://www.biorxiv.org/content/10.64898/2026.05.28.728381v1
Which might be OK if you are studying anxiety*, but the problem is that all kinds of other mental health problems would also be accompanied by anxiety so the rsfMRI differences might be entirely non-specific to your disorder of interest...
June 28, 2026 at 1:52 PM
Which might be OK if you are studying anxiety*, but the problem is that all kinds of other mental health problems would also be accompanied by anxiety so the rsfMRI differences might be entirely non-specific to your disorder of interest...
🔥CAN YOU MAP BLOOD FLOW in the brain from resting state fMRI?
🔥Ingenious new method [1] learns from jointly collected ASL (arterial spin labeling), SPECT, and rsFMRI to infer blood flow from fMRI
💡Cool as you can now estimate perfusion from 10000s of scans, of people who don't have ASL or SPECT 👇
🔥Ingenious new method [1] learns from jointly collected ASL (arterial spin labeling), SPECT, and rsFMRI to infer blood flow from fMRI
💡Cool as you can now estimate perfusion from 10000s of scans, of people who don't have ASL or SPECT 👇
August 23, 2025 at 5:18 PM
🔥CAN YOU MAP BLOOD FLOW in the brain from resting state fMRI?
🔥Ingenious new method [1] learns from jointly collected ASL (arterial spin labeling), SPECT, and rsFMRI to infer blood flow from fMRI
💡Cool as you can now estimate perfusion from 10000s of scans, of people who don't have ASL or SPECT 👇
🔥Ingenious new method [1] learns from jointly collected ASL (arterial spin labeling), SPECT, and rsFMRI to infer blood flow from fMRI
💡Cool as you can now estimate perfusion from 10000s of scans, of people who don't have ASL or SPECT 👇
Phosphorylated α-synuclein pS129 is found in aggregates that are pathological hallmarks of PD and DLB. The toxicity of pS129 has been up for debate for years. Combining LSM, MRI, rsfMRI and task fMRI, we demonstrate a toxic role for pS129 in synucleinopathies. 1/2
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Phosphorylated ⍺-Synuclein shapes changes in brain structure, task-related activity and functional connectivity in M83 mice
Phosphorylated α-synuclein at S129 (pS129) is the predominant form of α-synuclein in the aggregates known as Lewy bodies (LB) and Lewy neurites (LN), the pathological hallmarks of Parkinson's disease ...
www.biorxiv.org
September 23, 2026 at 2:01 PM
Phosphorylated α-synuclein pS129 is found in aggregates that are pathological hallmarks of PD and DLB. The toxicity of pS129 has been up for debate for years. Combining LSM, MRI, rsfMRI and task fMRI, we demonstrate a toxic role for pS129 in synucleinopathies. 1/2
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
I'm celebrating my Friday by reading this recent review published in @nature.com by @lucinauddin.bsky.social and Bharat Biswal on the history and future of rsfMRI. It's a great read for anybody interested! 🧪 www.nature.com/articles/s41...
The history and future of resting-state functional magnetic resonance imaging - Nature
This Review provides an overview of the history of resting-state functional MRI research, which has helped to reveal the spatiotemporal organization of the brain, and discusses how it can contribute f...
www.nature.com
May 30, 2025 at 6:31 PM
I'm celebrating my Friday by reading this recent review published in @nature.com by @lucinauddin.bsky.social and Bharat Biswal on the history and future of rsfMRI. It's a great read for anybody interested! 🧪 www.nature.com/articles/s41...
Retention and data exclusion challenges for representative longitudinal neuroimaging in the understanding of addiction www.biorxiv.org/content/10.1... - new preprint by @jocelynricard.bsky.social with Keith Humphreys
Retention and data exclusion challenges for representative longitudinal neuroimaging in the understanding of addiction
Head motion during resting-state functional magnetic resonance imaging (rsfMRI) poses a major challenge for neuroimaging research, often leading to data quality concerns and participant exclusions, pa...
www.biorxiv.org
September 10, 2025 at 1:54 PM
Retention and data exclusion challenges for representative longitudinal neuroimaging in the understanding of addiction www.biorxiv.org/content/10.1... - new preprint by @jocelynricard.bsky.social with Keith Humphreys
New pre-print from @alexfornito.bsky.social, James Pang, and myself, looking at the effects of rs-fMRI pre-processing pipelines on FC quality and behavioural predictions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The efficacy of resting-state fMRI denoising pipelines for motion correction and behavioural prediction.
Resting state functional magnetic resonance imaging (rsfMRI) is a pivotal tool for mapping the functional organization of the brain and its relation to individual differences in behaviour. One challen...
www.biorxiv.org
December 3, 2024 at 9:54 PM
New pre-print from @alexfornito.bsky.social, James Pang, and myself, looking at the effects of rs-fMRI pre-processing pipelines on FC quality and behavioural predictions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Maria Picó-Pérez, Ph.D.: Increased connectivity in salience/interoception networks (front-insular/ fronto-limbic) in OCD = associated with better CBT response; decreased rsfMRI connectivity is associated with better psychopharm response #ACNP2024
December 10, 2024 at 10:27 PM
Maria Picó-Pérez, Ph.D.: Increased connectivity in salience/interoception networks (front-insular/ fronto-limbic) in OCD = associated with better CBT response; decreased rsfMRI connectivity is associated with better psychopharm response #ACNP2024
As cognitive neuroscientists we prefer task-based neuroimaging. Most lifespan and Alzheimer's studies are restricted to resting-state fMRI. Our Nature Reviews Neuroscience comment led by @loopyluppi.bsky.social discusses how to reveal cognitive states from rsfMRI
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Unlocking spontaneous cognition in the age of data science - Nature Reviews Neuroscience
Spontaneous brain activity is experimentally unconstrained. Embracing this freedom unlocks rich opportunities beyond task-based and naturalistic paradigms, the traditional Herculean pillars of constra...
www.nature.com
July 18, 2026 at 1:26 PM
As cognitive neuroscientists we prefer task-based neuroimaging. Most lifespan and Alzheimer's studies are restricted to resting-state fMRI. Our Nature Reviews Neuroscience comment led by @loopyluppi.bsky.social discusses how to reveal cognitive states from rsfMRI
www.nature.com/articles/s41...
www.nature.com/articles/s41...
rsfMRI of the claustrum in 234 scans in awake marmosets, now in press at @imagingneurosci.bsky.social
like we showed in humans, rats, and mice previously, claustrum has widespread connectivity to the cortex, especially prefrontal, cingulate, and posterior parietal
direct.mit.edu/imag/article...
like we showed in humans, rats, and mice previously, claustrum has widespread connectivity to the cortex, especially prefrontal, cingulate, and posterior parietal
direct.mit.edu/imag/article...
August 1, 2025 at 4:20 PM
rsfMRI of the claustrum in 234 scans in awake marmosets, now in press at @imagingneurosci.bsky.social
like we showed in humans, rats, and mice previously, claustrum has widespread connectivity to the cortex, especially prefrontal, cingulate, and posterior parietal
direct.mit.edu/imag/article...
like we showed in humans, rats, and mice previously, claustrum has widespread connectivity to the cortex, especially prefrontal, cingulate, and posterior parietal
direct.mit.edu/imag/article...
📢 New in NeuroImage:
“Aphasia severity prediction using a multi-modal machine learning approach”
by Xinyi Hu, Maria Varkanitsa, Emerson Kropp, Margrit Betke, Prakash Ishwar & Swathi Kiran
🔗 doi.org/10.1016/j.ne...
#Aphasia #NeuroAI #StrokeRecovery
“Aphasia severity prediction using a multi-modal machine learning approach”
by Xinyi Hu, Maria Varkanitsa, Emerson Kropp, Margrit Betke, Prakash Ishwar & Swathi Kiran
🔗 doi.org/10.1016/j.ne...
#Aphasia #NeuroAI #StrokeRecovery
Aphasia severity prediction using a multi-modal machine learning approach
The present study examined an integrated multiple neuroimaging modality (T1 structural, Diffusion Tensor Imaging (DTI), and resting-state FMRI (rsFMRI…
doi.org
August 21, 2025 at 12:44 AM
📢 New in NeuroImage:
“Aphasia severity prediction using a multi-modal machine learning approach”
by Xinyi Hu, Maria Varkanitsa, Emerson Kropp, Margrit Betke, Prakash Ishwar & Swathi Kiran
🔗 doi.org/10.1016/j.ne...
#Aphasia #NeuroAI #StrokeRecovery
“Aphasia severity prediction using a multi-modal machine learning approach”
by Xinyi Hu, Maria Varkanitsa, Emerson Kropp, Margrit Betke, Prakash Ishwar & Swathi Kiran
🔗 doi.org/10.1016/j.ne...
#Aphasia #NeuroAI #StrokeRecovery
A new open source nonsurgical head restraint for awake mouse fMRI from our lab led by Sam Laxer. TL;DR Scanning about 25% longer than with a surgically implanted head post, combined with some training gives good results. Happy mice = happy rsfmri networks. direct.mit.edu/imag/article...
A non-invasive approach to awake mouse fMRI compatible with multi-modal techniques
Abstract. Mouse functional magnetic resonance imaging (fMRI) studies contribute significantly to basic fundamental and translational neuroscience research. Performing fMRI in awake mice could facilita...
direct.mit.edu
September 22, 2025 at 9:13 PM
A new open source nonsurgical head restraint for awake mouse fMRI from our lab led by Sam Laxer. TL;DR Scanning about 25% longer than with a surgically implanted head post, combined with some training gives good results. Happy mice = happy rsfmri networks. direct.mit.edu/imag/article...
Motion Insensitive Resting-State Analysis (MIRA): meet me at poster 1595 at #OHBM2025 to discuss a new way of performing motion correction for resting state fMRI that effectively removes the confounding effect of motion on rsfMRI derived correlation matrices!
June 26, 2025 at 11:29 PM
Motion Insensitive Resting-State Analysis (MIRA): meet me at poster 1595 at #OHBM2025 to discuss a new way of performing motion correction for resting state fMRI that effectively removes the confounding effect of motion on rsfMRI derived correlation matrices!
🚀 My first PhD paper is on arXiv! We present TReND, a self-supervised framework for neonatal brain parcellation, unveiling 7- & 19-network atlases for early neurodevelopment.
Paper Link: soveshmohapatra.com/research/TRe...
#Neuroimaging #rsfMRI #DeepLearning #NeonatalBrain #Brain
Paper Link: soveshmohapatra.com/research/TRe...
#Neuroimaging #rsfMRI #DeepLearning #NeonatalBrain #Brain
March 6, 2025 at 3:25 AM
🚀 My first PhD paper is on arXiv! We present TReND, a self-supervised framework for neonatal brain parcellation, unveiling 7- & 19-network atlases for early neurodevelopment.
Paper Link: soveshmohapatra.com/research/TRe...
#Neuroimaging #rsfMRI #DeepLearning #NeonatalBrain #Brain
Paper Link: soveshmohapatra.com/research/TRe...
#Neuroimaging #rsfMRI #DeepLearning #NeonatalBrain #Brain
New preprint
When I started contributing to the field of dance neuroscience, there was only a case study on the neural impact of dance in Parkinson’s. Incredible to share our randomized, controlled trial with 57 participants using rsfMRI pre- and post-intervention.
www.medrxiv.org/content/10.6...
When I started contributing to the field of dance neuroscience, there was only a case study on the neural impact of dance in Parkinson’s. Incredible to share our randomized, controlled trial with 57 participants using rsfMRI pre- and post-intervention.
www.medrxiv.org/content/10.6...
Leader and Follower Roles in Adapted Tango Reveal Complementary Neural Routes to Motor Improvement in Parkinson’s Disease
Parkinson’s disease (PD) disrupts internally generated (IG) movement through impaired striato-thalamo-cortical circuitry, while externally guided (EG) movement may recruit relatively preserved cerebel...
www.medrxiv.org
September 23, 2026 at 3:54 PM
New preprint
When I started contributing to the field of dance neuroscience, there was only a case study on the neural impact of dance in Parkinson’s. Incredible to share our randomized, controlled trial with 57 participants using rsfMRI pre- and post-intervention.
www.medrxiv.org/content/10.6...
When I started contributing to the field of dance neuroscience, there was only a case study on the neural impact of dance in Parkinson’s. Incredible to share our randomized, controlled trial with 57 participants using rsfMRI pre- and post-intervention.
www.medrxiv.org/content/10.6...
I think rsfMRI is perfectly valid, it's just overused. The problem is it's so easy - if you have 5 minutes spare scanner time you can just add it to any study.
Also, I bet rsfMRI differences between groups usually reflect differences in alertness and emotional state more than anything specific
Also, I bet rsfMRI differences between groups usually reflect differences in alertness and emotional state more than anything specific
June 26, 2026 at 1:20 PM
I think rsfMRI is perfectly valid, it's just overused. The problem is it's so easy - if you have 5 minutes spare scanner time you can just add it to any study.
Also, I bet rsfMRI differences between groups usually reflect differences in alertness and emotional state more than anything specific
Also, I bet rsfMRI differences between groups usually reflect differences in alertness and emotional state more than anything specific
🔥agrees pretty well with ASL or SPECT, when those were collected in the same people
🤯☣️No deep learning (!)
💡SVM is used, input is the time-series spectrum of the rsFMRI at each voxel in the brain
💡Includes segmented T1-weighted image for partial volume correction
🤯☣️No deep learning (!)
💡SVM is used, input is the time-series spectrum of the rsFMRI at each voxel in the brain
💡Includes segmented T1-weighted image for partial volume correction
August 23, 2025 at 5:18 PM
🔥agrees pretty well with ASL or SPECT, when those were collected in the same people
🤯☣️No deep learning (!)
💡SVM is used, input is the time-series spectrum of the rsFMRI at each voxel in the brain
💡Includes segmented T1-weighted image for partial volume correction
🤯☣️No deep learning (!)
💡SVM is used, input is the time-series spectrum of the rsFMRI at each voxel in the brain
💡Includes segmented T1-weighted image for partial volume correction
Another paper off the press! @isaacfalconer @MVarkanitsa @CORTEXjournal
shorturl.at/hsEL4 rsFMRI and functional connectivity changes in response to #aphasia #treatment #rehabilitation
shorturl.at/hsEL4 rsFMRI and functional connectivity changes in response to #aphasia #treatment #rehabilitation
March 10, 2024 at 1:00 PM
Another paper off the press! @isaacfalconer @MVarkanitsa @CORTEXjournal
shorturl.at/hsEL4 rsFMRI and functional connectivity changes in response to #aphasia #treatment #rehabilitation
shorturl.at/hsEL4 rsFMRI and functional connectivity changes in response to #aphasia #treatment #rehabilitation
Resting-state fMRI is still one of the most active areas in the field. ICA, seed-based connectivity, graph theory — the methods keep growing. Find rs-fMRI tools on NITRC. 💡 #rsfMRI #RestingState #Neuroimaging
NITRC: Search
www.nitrc.org
September 17, 2026 at 1:00 PM
Resting-state fMRI is still one of the most active areas in the field. ICA, seed-based connectivity, graph theory — the methods keep growing. Find rs-fMRI tools on NITRC. 💡 #rsfMRI #RestingState #Neuroimaging
Great overview!
V. important section is about controversies: confounds for resting-state fMRI are movement and physiological factors, such as cardiovascular activity and breathing.
I wonder what share of the rsfMRI signal can be explain by these confounds.
V. important section is about controversies: confounds for resting-state fMRI are movement and physiological factors, such as cardiovascular activity and breathing.
I wonder what share of the rsfMRI signal can be explain by these confounds.
When I first started working with resting state fMRI as a postdoc, there was a lot of skepticism about what we could learn from it. 20 years later, it's hard to imagine where the field of neuroscience would be without it. Here's a summary 🧠 www.nature.com/articles/s41...
The history and future of resting-state functional magnetic resonance imaging - Nature
This Review provides an overview of the history of resting-state functional MRI research, which has helped to reveal the spatiotemporal organization of the brain, and discusses how it can contribute f...
www.nature.com
May 29, 2025 at 1:40 PM
Great overview!
V. important section is about controversies: confounds for resting-state fMRI are movement and physiological factors, such as cardiovascular activity and breathing.
I wonder what share of the rsfMRI signal can be explain by these confounds.
V. important section is about controversies: confounds for resting-state fMRI are movement and physiological factors, such as cardiovascular activity and breathing.
I wonder what share of the rsfMRI signal can be explain by these confounds.
I wish this article mentioned that many of the patterns observed in psychedelic fMRI studies (e.g. increased Lempel-Ziv complexity, entropy etc) have also been observed in M/EEG studies. There's more going on in psychedelic science than just rsfMRI studies.
October 29, 2025 at 7:08 PM
I wish this article mentioned that many of the patterns observed in psychedelic fMRI studies (e.g. increased Lempel-Ziv complexity, entropy etc) have also been observed in M/EEG studies. There's more going on in psychedelic science than just rsfMRI studies.