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...
That is a legendary place. Enjoy!
October 6, 2025 at 12:44 PM
That is a legendary place. Enjoy!
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.
Well, scheduling change and *update* on dates: They will now be Sep 26, 29 and 30th, 2025. Hope that still works for those wanting to attend! Apologies for the confusion.
September 2, 2025 at 7:30 PM
Well, scheduling change and *update* on dates: They will now be Sep 26, 29 and 30th, 2025. Hope that still works for those wanting to attend! Apologies for the confusion.
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!
InstaCorr for instant enlightenment! This is a very powerful implementation in Ida, esp. with how it behaves with hi-res data. Take it for a spin, today!
August 5, 2025 at 12:06 AM
InstaCorr for instant enlightenment! This is a very powerful implementation in Ida, esp. with how it behaves with hi-res data. Take it for a spin, today!
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 only binary decision that is good here: *do* use transparent thresholding, yes!
April 12, 2025 at 8:56 PM
The only binary decision that is good here: *do* use transparent thresholding, yes!
Well, you were a very early adopter of this, thanks for working on this and continuing to push for better thresholding/visualizations so many years later.
April 12, 2025 at 4:04 PM
Well, you were a very early adopter of this, thanks for working on this and continuing to push for better thresholding/visualizations so many years later.
A lot of work to put together, but it was fun and educational (for me at least!). Thanks for adding a lot of careful argumentation and statistical insight, in particular.
April 12, 2025 at 4:02 PM
A lot of work to put together, but it was fun and educational (for me at least!). Thanks for adding a lot of careful argumentation and statistical insight, in particular.
Great to work with you on this. I think is almost exactly a year since we were Bootcamping with you in Querétaro? Looking forward to the next collaboration!
April 12, 2025 at 3:57 PM
Great to work with you on this. I think is almost exactly a year since we were Bootcamping with you in Querétaro? Looking forward to the next collaboration!
Ah, shining a Bright light on the data---sounds excellent!
Glad to collaborate on this, thanks @brightmg.bsky.social .
Glad to collaborate on this, thanks @brightmg.bsky.social .
April 11, 2025 at 8:34 PM
Ah, shining a Bright light on the data---sounds excellent!
Glad to collaborate on this, thanks @brightmg.bsky.social .
Glad to collaborate on this, thanks @brightmg.bsky.social .
Indeed, I thought "Revenge of the Dead Salmon" might have been a good subtitle, but it is actually bringing a positive message, so that didn't fit...
April 11, 2025 at 8:32 PM
Indeed, I thought "Revenge of the Dead Salmon" might have been a good subtitle, but it is actually bringing a positive message, so that didn't fit...
and @manshu.bsky.social , also should have found this handle to add earlier
April 11, 2025 at 8:30 PM
and @manshu.bsky.social , also should have found this handle to add earlier