Thomas Nichols
@nichols.bsky.social
Professor of Neuroimaging Statistics
Oxford Big Data Institute
Nuffield Department of Population Health
University of Oxford
Oxford Big Data Institute
Nuffield Department of Population Health
University of Oxford
Reposted by Thomas Nichols
Excited to share our manuscript about BrainEffeX, a tool for exploring fMRI effect sizes. Includes why we made it, how to use it + contribute, and how we made it.
@sneuroble.bsky.social @psychonetrics.bsky.social
@alexkfischbach.bsky.social
@nichols.bsky.social
@dscheinost.bsky.social & MINDS Lab
@sneuroble.bsky.social @psychonetrics.bsky.social
@alexkfischbach.bsky.social
@nichols.bsky.social
@dscheinost.bsky.social & MINDS Lab
Shearer et al. introduce an interactive web application for exploring fMRI effect maps:
doi.org/10.52294/001...
@halleeshearer.bsky.social @sneuroble.bsky.social @ohbmossig.bsky.social
#OpenDatasets #SpecialIssue
doi.org/10.52294/001...
@halleeshearer.bsky.social @sneuroble.bsky.social @ohbmossig.bsky.social
#OpenDatasets #SpecialIssue
November 12, 2025 at 7:46 PM
Excited to share our manuscript about BrainEffeX, a tool for exploring fMRI effect sizes. Includes why we made it, how to use it + contribute, and how we made it.
@sneuroble.bsky.social @psychonetrics.bsky.social
@alexkfischbach.bsky.social
@nichols.bsky.social
@dscheinost.bsky.social & MINDS Lab
@sneuroble.bsky.social @psychonetrics.bsky.social
@alexkfischbach.bsky.social
@nichols.bsky.social
@dscheinost.bsky.social & MINDS Lab
Reposted by Thomas Nichols
Ten Simple Rules for AI-Assisted Coding in Science arxiv.org/abs/2510.22254 - our latest, led by @ericwbridgeford.bsky.social
Ten Simple Rules for AI-Assisted Coding in Science
While AI coding tools have demonstrated potential to accelerate software development, their use in scientific computing raises critical questions about code quality and scientific validity. In this pa...
arxiv.org
October 28, 2025 at 1:12 PM
Ten Simple Rules for AI-Assisted Coding in Science arxiv.org/abs/2510.22254 - our latest, led by @ericwbridgeford.bsky.social
Happy to be a part of Anya Topiwala's new work, using Mendelian Randomisation with @ukbiobank.bsky.social & Million Veteran Program, finding that even modest alcohol consumption increases risk of dementia. ebm.bmj.com/content/earl...
Alcohol use and risk of dementia in diverse populations: evidence from cohort, case–control and Mendelian randomisation approaches
Objectives To investigate the relationship between alcohol consumption and dementia.
Design Prospective cohort and case–control analyses combined with linear and non-linear Mendelian randomisation.
...
ebm.bmj.com
September 25, 2025 at 7:27 AM
Happy to be a part of Anya Topiwala's new work, using Mendelian Randomisation with @ukbiobank.bsky.social & Million Veteran Program, finding that even modest alcohol consumption increases risk of dementia. ebm.bmj.com/content/earl...
Reposted by Thomas Nichols
𝐂𝐚𝐥𝐥 𝐟𝐨𝐫 𝐏𝐚𝐩𝐞𝐫𝐬 – 𝐒𝐩𝐚𝐭𝐢𝐚𝐥 𝐒𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐬 𝐢𝐧 𝐈𝐦𝐚𝐠𝐢𝐧𝐠
Special issue of 𝘚𝘵𝘢𝘵𝘪𝘴𝘵𝘪𝘤𝘴 𝘢𝘯𝘥 𝘋𝘢𝘵𝘢 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘪𝘯 𝘐𝘮𝘢𝘨𝘪𝘯𝘨, supported by @amstatnews.bsky.social ASA Sections on Statistics and the Environment (ENVR) and Statistics in Epidemiology (SIE)
Submission details:
tinyurl.com/47enwhwz
Special issue of 𝘚𝘵𝘢𝘵𝘪𝘴𝘵𝘪𝘤𝘴 𝘢𝘯𝘥 𝘋𝘢𝘵𝘢 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘪𝘯 𝘐𝘮𝘢𝘨𝘪𝘯𝘨, supported by @amstatnews.bsky.social ASA Sections on Statistics and the Environment (ENVR) and Statistics in Epidemiology (SIE)
Submission details:
tinyurl.com/47enwhwz
August 28, 2025 at 4:38 PM
𝐂𝐚𝐥𝐥 𝐟𝐨𝐫 𝐏𝐚𝐩𝐞𝐫𝐬 – 𝐒𝐩𝐚𝐭𝐢𝐚𝐥 𝐒𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐬 𝐢𝐧 𝐈𝐦𝐚𝐠𝐢𝐧𝐠
Special issue of 𝘚𝘵𝘢𝘵𝘪𝘴𝘵𝘪𝘤𝘴 𝘢𝘯𝘥 𝘋𝘢𝘵𝘢 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘪𝘯 𝘐𝘮𝘢𝘨𝘪𝘯𝘨, supported by @amstatnews.bsky.social ASA Sections on Statistics and the Environment (ENVR) and Statistics in Epidemiology (SIE)
Submission details:
tinyurl.com/47enwhwz
Special issue of 𝘚𝘵𝘢𝘵𝘪𝘴𝘵𝘪𝘤𝘴 𝘢𝘯𝘥 𝘋𝘢𝘵𝘢 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘪𝘯 𝘐𝘮𝘢𝘨𝘪𝘯𝘨, supported by @amstatnews.bsky.social ASA Sections on Statistics and the Environment (ENVR) and Statistics in Epidemiology (SIE)
Submission details:
tinyurl.com/47enwhwz
Epic work led by Habib Ganjgahi is out in Nature Medicine... data-driven clustering of MS finds 3 distinct states, early/mild, active, advanced, w/ transition to the advanced state only occuring through the active state... replicated twice!
doi.org/10.1038/s415...
doi.org/10.1038/s415...
August 20, 2025 at 12:15 PM
Epic work led by Habib Ganjgahi is out in Nature Medicine... data-driven clustering of MS finds 3 distinct states, early/mild, active, advanced, w/ transition to the advanced state only occuring through the active state... replicated twice!
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Thomas Nichols
Really nice study, and extends some of the ideas developed in this paper pubmed.ncbi.nlm.nih.gov/32673043/
1/11 Excited to share our @Naturestudy led by @leonooi.bsky.social @csabaorban.bsky.social @shaoshiz.bsky.social
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
July 17, 2025 at 2:46 PM
Really nice study, and extends some of the ideas developed in this paper pubmed.ncbi.nlm.nih.gov/32673043/
For me, this work is a classic @ohbmofficial.bsky.social story: In 2023 I wasn't working with @bttyeo.bsky.social but I overheard him at his poster pointing to some accuracy curves saying "I don't why they have this particular shape". That kicked off the collab that led to these results.
3/11 Tom's model explains empirical prediction accuracies well across 76 phenotypes from 9 resting-fMRI & task-fMRI datasets (R2 = 0.89), spanning many scanners, acquisitions, racial groups, disorders & ages.
Does this mean that we should collect large datasets with short scans?
Does this mean that we should collect large datasets with short scans?
July 17, 2025 at 6:34 AM
For me, this work is a classic @ohbmofficial.bsky.social story: In 2023 I wasn't working with @bttyeo.bsky.social but I overheard him at his poster pointing to some accuracy curves saying "I don't why they have this particular shape". That kicked off the collab that led to these results.
Reposted by Thomas Nichols
1/11 Excited to share our @Naturestudy led by @leonooi.bsky.social @csabaorban.bsky.social @shaoshiz.bsky.social
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
July 17, 2025 at 1:36 AM
1/11 Excited to share our @Naturestudy led by @leonooi.bsky.social @csabaorban.bsky.social @shaoshiz.bsky.social
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
AI performance is known to scale with logarithm of sample size (Kaplan 2020), but in many domains, sample size can be # participants or # measurements...
doi.org/10.1038/s415...
Wasn't aware of tinyplot... an overlay package to make base R graphics easier to use. While I use ggplot2 for some tasks there are many situations where I prefer base R plotting, and this tool will be super helpful in those seetings.
`tinyplot` v0.4.2 is now available on CRAN + R-universe 🎉 Mostly bug fixes, but includes some important integration improvements for Positron IDE users. Release notes: grantmcdermott.com/tinyplot/NEW...
#rstats
#rstats
July 13, 2025 at 1:18 PM
Wasn't aware of tinyplot... an overlay package to make base R graphics easier to use. While I use ggplot2 for some tasks there are many situations where I prefer base R plotting, and this tool will be super helpful in those seetings.
Reposted by Thomas Nichols
Looking forward to presenting our team's research on AI for EHR at The Big Data Institute at Oxford on July 10th at 2 pm! Thanks to Sumeeta and Prof @nichols.bsky.social for organising.
Link: talks.ox.ac.uk/talks/id/590...
Link: talks.ox.ac.uk/talks/id/590...
Artificial intelligence for electronic health records
For our next talk, in Machine Learning, we will be hearing from Dr Shishir Rao, Senior Research Scientist, Deep Medicine research group, NDWRH, University of Oxford. We’re delighted to host Shishir in...
talks.ox.ac.uk
July 4, 2025 at 12:38 PM
Looking forward to presenting our team's research on AI for EHR at The Big Data Institute at Oxford on July 10th at 2 pm! Thanks to Sumeeta and Prof @nichols.bsky.social for organising.
Link: talks.ox.ac.uk/talks/id/590...
Link: talks.ox.ac.uk/talks/id/590...
Reposted by Thomas Nichols
Excited to share our latest preprint: "Neurosynth Compose: A Web-Based Platform for Flexible and Reproducible Neuroimaging Meta-Analysis"
Here, we cover the why, what, and how of the next generation Neurosynth ecosystem for reproducible neuroimaging meta-analysis.
osf.io/preprints/os...
Here, we cover the why, what, and how of the next generation Neurosynth ecosystem for reproducible neuroimaging meta-analysis.
osf.io/preprints/os...
OSF
osf.io
July 9, 2025 at 6:20 PM
Excited to share our latest preprint: "Neurosynth Compose: A Web-Based Platform for Flexible and Reproducible Neuroimaging Meta-Analysis"
Here, we cover the why, what, and how of the next generation Neurosynth ecosystem for reproducible neuroimaging meta-analysis.
osf.io/preprints/os...
Here, we cover the why, what, and how of the next generation Neurosynth ecosystem for reproducible neuroimaging meta-analysis.
osf.io/preprints/os...
Almost recovered from #OHBM2025... has anyone else found the E-posters nearly imposible to find. They are here, discoverable through the app and the browser-link-out button
ww6.aievolution.com/hbm2501/inde...
ww6.aievolution.com/hbm2501/inde...
July 3, 2025 at 1:46 PM
Almost recovered from #OHBM2025... has anyone else found the E-posters nearly imposible to find. They are here, discoverable through the app and the browser-link-out button
ww6.aievolution.com/hbm2501/inde...
ww6.aievolution.com/hbm2501/inde...
Public service announcement: Don’t forget to upload your #OHBM2025 poster PDF, at ww6.aievolution.com/hbm2501/
OHBM - 2025 - Speaker Sign In
ww6.aievolution.com
June 26, 2025 at 11:20 PM
Public service announcement: Don’t forget to upload your #OHBM2025 poster PDF, at ww6.aievolution.com/hbm2501/
Reposted by Thomas Nichols
The beta release of SPM-Python is out now! Amazing work by Johan Medrano @johmedr.bsky.social , Yael Balbastre, Yulia Bezsudnova @ybezs.bsky.social and other members of their team. A new era for SPM! #OHBM2025
Drumroll... The SPM team will announce that SPM is now fully accessible from Python! 🐍 Learn more about SPM-Python at the SPM roundtable event (Friday, 1pm) and poster number 1841 at #OHBM2025. Try the beta for yourself at github.com/spm/spm-python [2/7]
GitHub - spm/spm-python: The Python interface to SPM
The Python interface to SPM. Contribute to spm/spm-python development by creating an account on GitHub.
github.com
June 23, 2025 at 8:22 AM
The beta release of SPM-Python is out now! Amazing work by Johan Medrano @johmedr.bsky.social , Yael Balbastre, Yulia Bezsudnova @ybezs.bsky.social and other members of their team. A new era for SPM! #OHBM2025
Reposted by Thomas Nichols
Interested in practical tips for assessing collinearity and why common fixes might not help? Come to the #OHBM2025 oral session Friday at 11:30AM (P2)! I’ll share simulation results and @demidenko.bsky.social will present real data. Also, check out my poster Thursday (1051)!
June 25, 2025 at 10:04 PM
Interested in practical tips for assessing collinearity and why common fixes might not help? Come to the #OHBM2025 oral session Friday at 11:30AM (P2)! I’ll share simulation results and @demidenko.bsky.social will present real data. Also, check out my poster Thursday (1051)!
Is anyone else at #OHBM2024 educational courses maddened by the lack of time per-course schedule? In the app, the individual talks are listed *alphabetically* by talk title, all with the same start time. Same thing for symposia...
June 24, 2025 at 12:52 AM
Is anyone else at #OHBM2024 educational courses maddened by the lack of time per-course schedule? In the app, the individual talks are listed *alphabetically* by talk title, all with the same start time. Same thing for symposia...
Useful #OHBM2024 deep link - Table listing all posters with stand-by times & categories
gmpartners365-my.sharepoint.com/:x:/g/person...
gmpartners365-my.sharepoint.com/:x:/g/person...
Sign in to your account
gmpartners365-my.sharepoint.com
June 24, 2025 at 12:20 AM
Useful #OHBM2024 deep link - Table listing all posters with stand-by times & categories
gmpartners365-my.sharepoint.com/:x:/g/person...
gmpartners365-my.sharepoint.com/:x:/g/person...
At #OHBM2025 the Open Science Room has been squeezed and next year is at risk of being dramatically reduced/cut. If you like the OSR please consider signing/sharing this petition! chng.it/yjs4Bnyf9s
@ohbmofficial.bsky.social @ohbmossig.bsky.social
@ohbmofficial.bsky.social @ohbmossig.bsky.social
Preserve the Open Science Room at the Organization for Human Brain Mapping Annual Meeting
Can you spare a minute to help this campaign?
chng.it
June 18, 2025 at 9:10 AM
At #OHBM2025 the Open Science Room has been squeezed and next year is at risk of being dramatically reduced/cut. If you like the OSR please consider signing/sharing this petition! chng.it/yjs4Bnyf9s
@ohbmofficial.bsky.social @ohbmossig.bsky.social
@ohbmofficial.bsky.social @ohbmossig.bsky.social
Reposted by Thomas Nichols
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
Happy to see Julio Peraza's lastest posted, "NiCLIP", using a CLIP model to improve 'reverse inference' prediction of task fMRI results based on peak coordinate data www.biorxiv.org/content/10.1... w/ @angielaird.bsky.social @neurozorro.bsky.social James Kent & JB Poline
www.biorxiv.org
June 16, 2025 at 6:14 PM
Happy to see Julio Peraza's lastest posted, "NiCLIP", using a CLIP model to improve 'reverse inference' prediction of task fMRI results based on peak coordinate data www.biorxiv.org/content/10.1... w/ @angielaird.bsky.social @neurozorro.bsky.social James Kent & JB Poline
Reposted by Thomas Nichols
Happy to see my first first-author paper in Imaging Neuroscience (along with @fmrib-karla.bsky.social and @nichols.bsky.social):
Characterising ongoing brain aging and baseline effects from cross-sectional data
doi.org/10.1162/IMAG...
Characterising ongoing brain aging and baseline effects from cross-sectional data
doi.org/10.1162/IMAG...
May 29, 2025 at 5:16 AM
Happy to see my first first-author paper in Imaging Neuroscience (along with @fmrib-karla.bsky.social and @nichols.bsky.social):
Characterising ongoing brain aging and baseline effects from cross-sectional data
doi.org/10.1162/IMAG...
Characterising ongoing brain aging and baseline effects from cross-sectional data
doi.org/10.1162/IMAG...
Reposted by Thomas Nichols
Registration Open! FSL Course 2025 will be held fully online, 15th – 26th September. Details & registration info here: open.win.ox.ac.uk/pages/fslcou...
The course covers lectures & hands-on practicals on structural, functional, diffusion and resting state brain image analysis.
The course covers lectures & hands-on practicals on structural, functional, diffusion and resting state brain image analysis.
May 8, 2025 at 8:34 AM
Registration Open! FSL Course 2025 will be held fully online, 15th – 26th September. Details & registration info here: open.win.ox.ac.uk/pages/fslcou...
The course covers lectures & hands-on practicals on structural, functional, diffusion and resting state brain image analysis.
The course covers lectures & hands-on practicals on structural, functional, diffusion and resting state brain image analysis.
Reposted by Thomas Nichols
🤔 You’d like to share your research code but not sure how to…?
🔓*Very* excited to finally share this work led by @nicolasrougier.bsky.social in which we propose a practical set of guidelines for opening code.
inria.hal.science/hal-04930405...
🔓*Very* excited to finally share this work led by @nicolasrougier.bsky.social in which we propose a practical set of guidelines for opening code.
inria.hal.science/hal-04930405...
February 11, 2025 at 2:51 PM
🤔 You’d like to share your research code but not sure how to…?
🔓*Very* excited to finally share this work led by @nicolasrougier.bsky.social in which we propose a practical set of guidelines for opening code.
inria.hal.science/hal-04930405...
🔓*Very* excited to finally share this work led by @nicolasrougier.bsky.social in which we propose a practical set of guidelines for opening code.
inria.hal.science/hal-04930405...
Looks like a very useful tool...
Ru Kong, Lucina Q. Uddin A network correspondence toolbox for quantitative evaluation of novel neuroimaging results www.nature.com/articles/s41...
April 14, 2025 at 10:54 PM
Looks like a very useful tool...
Reposted by Thomas Nichols
Voets et al. outline best practice recommendations from the OHBM Working Group on clinical language fMRI mapping: doi.org/10.52294/001...
@cyrilrpernet.bsky.social @lindadouw.bsky.social @nichols.bsky.social @fmri-today.bsky.social @mallarchak.bsky.social @ohbmofficial.bsky.social
@cyrilrpernet.bsky.social @lindadouw.bsky.social @nichols.bsky.social @fmri-today.bsky.social @mallarchak.bsky.social @ohbmofficial.bsky.social
January 23, 2025 at 4:49 PM
Voets et al. outline best practice recommendations from the OHBM Working Group on clinical language fMRI mapping: doi.org/10.52294/001...
@cyrilrpernet.bsky.social @lindadouw.bsky.social @nichols.bsky.social @fmri-today.bsky.social @mallarchak.bsky.social @ohbmofficial.bsky.social
@cyrilrpernet.bsky.social @lindadouw.bsky.social @nichols.bsky.social @fmri-today.bsky.social @mallarchak.bsky.social @ohbmofficial.bsky.social