Paul Taylor
@afni-pt.bsky.social
Brain imaging methods at SSCC/NIMH/NIH, working in C/Python/tcsh, some astrophysics in world line, programming/processing lecturer at AIMS. All views my own.
Pinned
Paul Taylor
@afni-pt.bsky.social
· Sep 2
AFNI Bootcamp: Sep. 23-25, 2025 | afni.nimh.nih.gov
afni.nimh.nih.gov
Announcing the next AFNI Bootcamp: Sep 23-25, 2025.
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
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...
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...
November 17, 2025 at 8:15 PM
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...
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...
Thanks, @gangchen6.bsky.social for leading the charge on pointing out and detailing several really important things to think about at the heart of FMRI studies and interpretation.
Thanks to Zhengchen Cai, @kordinglab.bsky.social, Tom Liu, Josh Faskowitz, @fmri-today.bsky.social, Bharat Biswal, and @afni-pt.bsky.social for fueling this ride and helping turn it into a commentary.
September 24, 2025 at 12:57 AM
Thanks, @gangchen6.bsky.social for leading the charge on pointing out and detailing several really important things to think about at the heart of FMRI studies and interpretation.
Announcing the next AFNI Bootcamp: Sep 23-25, 2025.
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
AFNI Bootcamp: Sep. 23-25, 2025 | afni.nimh.nih.gov
afni.nimh.nih.gov
September 2, 2025 at 4:41 PM
Announcing the next AFNI Bootcamp: Sep 23-25, 2025.
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
Free, open & virtual.
This "Part 1" will focus on basic visualization and single subject FMRI processing, including discussions of alignment, templates, regression, ROIs and quality control.
Details & registration: afni.nimh.nih.gov/bootcamp
Reposted by Paul Taylor
If you’d like to write a commentary to accompany our new article arguing for a rethinking of how we approach understanding visual function in occipitotemporal cortex, now is your chance!
Our target discussion article out in Cognitive Neuroscience! It will be followed by peer commentary and our responses. If you would like to write a commentary, please reach out to the journal! 1/18 www.tandfonline.com/doi/full/10.... @cibaker.bsky.social @susanwardle.bsky.social
August 29, 2025 at 7:38 PM
If you’d like to write a commentary to accompany our new article arguing for a rethinking of how we approach understanding visual function in occipitotemporal cortex, now is your chance!
Cool work, and particularly after some recent discussions at OHBM, it is really nice to see all of transparent threshold, beta-weight overlay coloration and two-tailed tests used together in the results reporting. Helps me (and maybe others) see the whole picture clearly.
Excited to ✨share✨ that our paper on ✨sharing✨ is published! Across 3 studies that build on one another, we show that perceived alignment with one's peers increases the likelihood of information sharing.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Perceived community alignment increases information sharing - Nature Communications
Information sharing is a ubiquitous and consequential behavior. Here, the authors use neuroimaging and behavioral studies to show that people are driven to share information that they believe will be ...
www.nature.com
July 4, 2025 at 11:03 AM
Cool work, and particularly after some recent discussions at OHBM, it is really nice to see all of transparent threshold, beta-weight overlay coloration and two-tailed tests used together in the results reporting. Helps me (and maybe others) see the whole picture clearly.
Indeed, so happy to see this elegant article by @misicbata.bsky.social . It resonate and persuades.
This is what @afni-pt.bsky.social has been advocating for quite some time! And yes, they are splendid.
The splendour of unthresholded brain maps apertureneuro.org/article/1406...
July 1, 2025 at 11:56 AM
Indeed, so happy to see this elegant article by @misicbata.bsky.social . It resonate and persuades.
Reposted by Paul Taylor
Looking forward to #OHBM2025 in Brisbane next week! My lab is recruiting a postdoc & neuroimaging analyst/developer to support our NIH funded work in fMRI-based Alzheimer's biomarker development (NIA R01AG083919). Email or DM if you want to meet up in Brisbane! www.statmindlab.com/join-us
Home
What can we do with functional MRI data? For many years, fMRI has been used to discover population-level patterns of brain function, organization and connectivity, and to understand differences in t...
www.statmindlab.com
June 17, 2025 at 12:15 AM
Looking forward to #OHBM2025 in Brisbane next week! My lab is recruiting a postdoc & neuroimaging analyst/developer to support our NIH funded work in fMRI-based Alzheimer's biomarker development (NIA R01AG083919). Email or DM if you want to meet up in Brisbane! www.statmindlab.com/join-us
Reposted by Paul Taylor
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 28, 2025 at 3:52 PM
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...
**FMRI/neuroimaging folks**
Quick reminder @ the next AFNI Bootcamp: May 28-30, 2025. Learn through interactive data analysis!
Day 1-2: data viz, single subject analysis and QC.
Day 3: statistics, results reporting and group analysis.
Details, registration and schedule:
afni.nimh.nih.gov/bootcamp
Quick reminder @ the next AFNI Bootcamp: May 28-30, 2025. Learn through interactive data analysis!
Day 1-2: data viz, single subject analysis and QC.
Day 3: statistics, results reporting and group analysis.
Details, registration and schedule:
afni.nimh.nih.gov/bootcamp
May 22, 2025 at 6:42 PM
**FMRI/neuroimaging folks**
Quick reminder @ the next AFNI Bootcamp: May 28-30, 2025. Learn through interactive data analysis!
Day 1-2: data viz, single subject analysis and QC.
Day 3: statistics, results reporting and group analysis.
Details, registration and schedule:
afni.nimh.nih.gov/bootcamp
Quick reminder @ the next AFNI Bootcamp: May 28-30, 2025. Learn through interactive data analysis!
Day 1-2: data viz, single subject analysis and QC.
Day 3: statistics, results reporting and group analysis.
Details, registration and schedule:
afni.nimh.nih.gov/bootcamp
We are pleased to announce the next AFNI Bootcamp, May 28-30, 2025.
First 2 days: data visualization, single subject analysis and QC. 3rd day: statistics, results reporting and group analysis.
Please see here for details, registration link and preliminary schedule:
afni.nimh.nih.gov/bootcamp
First 2 days: data visualization, single subject analysis and QC. 3rd day: statistics, results reporting and group analysis.
Please see here for details, registration link and preliminary schedule:
afni.nimh.nih.gov/bootcamp
AFNI Bootcamp: May 28-30, 2025 | afni.nimh.nih.gov
afni.nimh.nih.gov
May 7, 2025 at 6:37 PM
We are pleased to announce the next AFNI Bootcamp, May 28-30, 2025.
First 2 days: data visualization, single subject analysis and QC. 3rd day: statistics, results reporting and group analysis.
Please see here for details, registration link and preliminary schedule:
afni.nimh.nih.gov/bootcamp
First 2 days: data visualization, single subject analysis and QC. 3rd day: statistics, results reporting and group analysis.
Please see here for details, registration link and preliminary schedule:
afni.nimh.nih.gov/bootcamp
Who knew that breathing was so important? Well, at least in FMRI it is... Nice work by @brightmg.bsky.social & Co!
Breath hold fMRI is great for measuring CVR... *except when your participant or patient doesn't quite perform the task the way you'd like. Let's see if we can fix that! (Spoiler, it looks like we can, using the respiratory belt data to predict or fill in missing PETCO2 data!)
New paper in Imaging Neuroscience by Rebecca G. Clements, Molly G. Bright, et al:
Quantitative mapping of cerebrovascular reactivity amplitude and delay with breath-hold BOLD fMRI when end-tidal CO2 quality is low
doi.org/10.1162/imag...
Quantitative mapping of cerebrovascular reactivity amplitude and delay with breath-hold BOLD fMRI when end-tidal CO2 quality is low
doi.org/10.1162/imag...
May 3, 2025 at 11:49 AM
Who knew that breathing was so important? Well, at least in FMRI it is... Nice work by @brightmg.bsky.social & Co!
Nice work, @gangchen6.bsky.social !
Should statistics respect
science more? Our third speaker Gang Chen (@gangchen6.bsky.social) argues that strict adherence to statistical conventions may obscure rather than clarify, and suggest ways in which rethink about how we model our data and report our results:
science more? Our third speaker Gang Chen (@gangchen6.bsky.social) argues that strict adherence to statistical conventions may obscure rather than clarify, and suggest ways in which rethink about how we model our data and report our results:
April 25, 2025 at 7:16 PM
Nice work, @gangchen6.bsky.social !
Reposted by Paul Taylor
"Highlight, don't hide" @gangchen6.bsky.social makes an impassioned argument that thresholding (reflective of a "binary" yes/no approach to analysis) holds back our science, making it less transparent and less reproducible.
Instead, be a facilitator - share uncertainty and evidence! #SANS2025
Instead, be a facilitator - share uncertainty and evidence! #SANS2025
April 25, 2025 at 4:11 PM
"Highlight, don't hide" @gangchen6.bsky.social makes an impassioned argument that thresholding (reflective of a "binary" yes/no approach to analysis) holds back our science, making it less transparent and less reproducible.
Instead, be a facilitator - share uncertainty and evidence! #SANS2025
Instead, be a facilitator - share uncertainty and evidence! #SANS2025
The result of a large (42 authors!) collaboration:
"Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation"
arxiv.org/abs/2504.07824
TL;DR: The FMRI world can (and should) improve results interpretation and reproducibility *today*, via transparent thresholding.
"Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation"
arxiv.org/abs/2504.07824
TL;DR: The FMRI world can (and should) improve results interpretation and reproducibility *today*, via transparent thresholding.
April 11, 2025 at 12:35 PM
The result of a large (42 authors!) collaboration:
"Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation"
arxiv.org/abs/2504.07824
TL;DR: The FMRI world can (and should) improve results interpretation and reproducibility *today*, via transparent thresholding.
"Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation"
arxiv.org/abs/2504.07824
TL;DR: The FMRI world can (and should) improve results interpretation and reproducibility *today*, via transparent thresholding.
Excellent folks to work with!
Likely hiring one postbac trainee for @fmri-today.bsky.social's Section on Functional Imaging Methods. Give the relatively later start time for the search, I'm not yet sure how quickly this search will happen. If you are interested, apply and reach out ASAP. fim.nimh.nih.gov
April 9, 2025 at 12:22 AM
Excellent folks to work with!
Reposted by Paul Taylor
Likely hiring one postbac trainee for @fmri-today.bsky.social's Section on Functional Imaging Methods. Give the relatively later start time for the search, I'm not yet sure how quickly this search will happen. If you are interested, apply and reach out ASAP. fim.nimh.nih.gov
April 8, 2025 at 8:12 PM
Likely hiring one postbac trainee for @fmri-today.bsky.social's Section on Functional Imaging Methods. Give the relatively later start time for the search, I'm not yet sure how quickly this search will happen. If you are interested, apply and reach out ASAP. fim.nimh.nih.gov
Do you like genes and estimating heritability? Then @gangchen6.bsky.social and D. Moraczewski have important news for you.
Conventional estimation methods ignore measurement error, leading to a bias. Don't worry: hierarchical modeling to the rescue!
www.frontiersin.org/journals/gen...
Conventional estimation methods ignore measurement error, leading to a bias. Don't worry: hierarchical modeling to the rescue!
www.frontiersin.org/journals/gen...
April 2, 2025 at 1:44 PM
Do you like genes and estimating heritability? Then @gangchen6.bsky.social and D. Moraczewski have important news for you.
Conventional estimation methods ignore measurement error, leading to a bias. Don't worry: hierarchical modeling to the rescue!
www.frontiersin.org/journals/gen...
Conventional estimation methods ignore measurement error, leading to a bias. Don't worry: hierarchical modeling to the rescue!
www.frontiersin.org/journals/gen...
Reposted by Paul Taylor
It's finally here! Use the Network Correspondence Toolbox to help contextualize your neuroimaging findings 🧠
A network correspondence toolbox for quantitative evaluation of novel neuroimaging results - Nature Communications
Here, the authors present the Network Correspondence Toolbox, which enables researchers to examine and report spatial correspondence between their neuroimaging results and widely used brain atlases.
www.nature.com
March 26, 2025 at 1:54 AM
It's finally here! Use the Network Correspondence Toolbox to help contextualize your neuroimaging findings 🧠
Pretty stunning!
In vivo reconstruction of Duvernoy's postmortem vasculature images
- Fast, high-res imaging: Whole-brain 0.35 mm MRI in <7 min at 7 T
- Vessel-type specific podt-processing: Capturing large leptomeningeal, pial, and intracortical meso-veins
PDF: doi.org/10.1101/2025...
- Fast, high-res imaging: Whole-brain 0.35 mm MRI in <7 min at 7 T
- Vessel-type specific podt-processing: Capturing large leptomeningeal, pial, and intracortical meso-veins
PDF: doi.org/10.1101/2025...
March 26, 2025 at 11:01 PM
Pretty stunning!
Reposted by Paul Taylor
New paper in Imaging Neuroscience by Catriona L. Scrivener and Edward H. Silson:
Opponent visuospatial coding structures responses during memory recall and visual perception in medial parietal cortex
doi.org/10.1162/imag...
Opponent visuospatial coding structures responses during memory recall and visual perception in medial parietal cortex
doi.org/10.1162/imag...
March 25, 2025 at 7:17 AM
New paper in Imaging Neuroscience by Catriona L. Scrivener and Edward H. Silson:
Opponent visuospatial coding structures responses during memory recall and visual perception in medial parietal cortex
doi.org/10.1162/imag...
Opponent visuospatial coding structures responses during memory recall and visual perception in medial parietal cortex
doi.org/10.1162/imag...
Reposted by Paul Taylor
Excited to announce the 500th paper published by Imaging Neuroscience ! @imagingneurosci.bsky.social @mitpress.bsky.social
We've come a long way in a short time and are hugely grateful to the neuroimaging community for your support.
Hope to see lots of you at OHBM @ohbmofficial.bsky.social
We've come a long way in a short time and are hugely grateful to the neuroimaging community for your support.
Hope to see lots of you at OHBM @ohbmofficial.bsky.social
New paper in Imaging Neuroscience by Britta U. Westner, Floris P. de Lange, et al:
Typical neural adaptation for familiar images in autistic adolescents
doi.org/10.1162/imag...
Typical neural adaptation for familiar images in autistic adolescents
doi.org/10.1162/imag...
March 20, 2025 at 6:48 AM
Excited to announce the 500th paper published by Imaging Neuroscience ! @imagingneurosci.bsky.social @mitpress.bsky.social
We've come a long way in a short time and are hugely grateful to the neuroimaging community for your support.
Hope to see lots of you at OHBM @ohbmofficial.bsky.social
We've come a long way in a short time and are hugely grateful to the neuroimaging community for your support.
Hope to see lots of you at OHBM @ohbmofficial.bsky.social
Reposted by Paul Taylor
People from my lab did a wonderful job on Brain Week teaching about the problems with substance use. A major effort on their part.
March 15, 2025 at 9:38 PM
People from my lab did a wonderful job on Brain Week teaching about the problems with substance use. A major effort on their part.
If anyone wants a fun activity in DC over the next couple months, The Textile Museum (at GW) is celebrating its 100th anniversary with an amazing set of, well, textiles from around the globe. Incredible craftsmanship, science, skill & cultural heritages on display. (Museum is free! Open Tue-Sat.)
March 11, 2025 at 12:23 PM
If anyone wants a fun activity in DC over the next couple months, The Textile Museum (at GW) is celebrating its 100th anniversary with an amazing set of, well, textiles from around the globe. Incredible craftsmanship, science, skill & cultural heritages on display. (Museum is free! Open Tue-Sat.)
Reposted by Paul Taylor
Today is amazing grad student Paul LaFosse's last lab meeting.
Here's cool data he showed: Paul used 2p holographic optogenetics (laser stim) to select and stimulate this neuron in a working brain.
This ability to change neural activity is key to understanding brains. To understanding #AI too. 🧪
Here's cool data he showed: Paul used 2p holographic optogenetics (laser stim) to select and stimulate this neuron in a working brain.
This ability to change neural activity is key to understanding brains. To understanding #AI too. 🧪
March 5, 2025 at 4:09 PM
Today is amazing grad student Paul LaFosse's last lab meeting.
Here's cool data he showed: Paul used 2p holographic optogenetics (laser stim) to select and stimulate this neuron in a working brain.
This ability to change neural activity is key to understanding brains. To understanding #AI too. 🧪
Here's cool data he showed: Paul used 2p holographic optogenetics (laser stim) to select and stimulate this neuron in a working brain.
This ability to change neural activity is key to understanding brains. To understanding #AI too. 🧪
Reposted by Paul Taylor
New preprint from the lab: www.biorxiv.org/content/10.1...
This was led by former Bachelor student Débora Elizarrarás and postdoc César Carranza. Here we wanted to study structural brain changes in opiod self-administration. Specifically if there was a link between MRI volume and neuroinflamation.
This was led by former Bachelor student Débora Elizarrarás and postdoc César Carranza. Here we wanted to study structural brain changes in opiod self-administration. Specifically if there was a link between MRI volume and neuroinflamation.
Morphine self-administration induces region-specific brain volume changes and microglial phenotypic alterations without affecting neuronal density in male Wistar rats
Addiction to opioids, including morphine, is a major public health crisis in the U.S. It has been associated with brain volume changes in reward-related regions, neuronal death, and neuroinflammation....
www.biorxiv.org
February 26, 2025 at 7:53 PM
New preprint from the lab: www.biorxiv.org/content/10.1...
This was led by former Bachelor student Débora Elizarrarás and postdoc César Carranza. Here we wanted to study structural brain changes in opiod self-administration. Specifically if there was a link between MRI volume and neuroinflamation.
This was led by former Bachelor student Débora Elizarrarás and postdoc César Carranza. Here we wanted to study structural brain changes in opiod self-administration. Specifically if there was a link between MRI volume and neuroinflamation.