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Baptiste Couvy-Duchesne

@baptistecd.bsky.social
231 followers 584 following 33 posts

Genetics, brain and more 🇦🇺🇫🇷 Working with the University of Queensland, Inria (France), Paris Brain Institute and QIMR Berghofer

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Reposted by Baptiste Couvy-Duchesne
Psychiatric Genomics Consortium (PGC) @pgcgenetics.bsky.social · 01/03/2026
🧵 New publication from the PGC Anxiety Working Group. Our GWAS meta-analysis of anxiety disorders is now published in @natgenet.nature.com! 🔗: doi.org/10.1038/s415...
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
Big shout out to @clarajiang.bsky.social for leading this work, to all co-authors in France, Australia and UK, to @iesinria.bsky.social, @institutducerveau.bsky.social, #UQ, #IMB, as well as the Inria Associate team funding who made the collaboration possible by funding Clara' exchange in France
project.inria.fr
Leveraging brain magnetic resonance images and genetics for neurodegenerative and psychiatric disorders – A modern web site
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
We concluded that depression does not have a strong signature in the grey matter, and that other brain MRI sequences (e.g. diffusion, or functional MRI) may be required to accurately predict depression.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
In our article, we estimated the morphometricity of depression to be 6%, which means that only 6% of the disease status variance is captured by all brain measurements. This implies that an optimal linear predictor would only reach an AUC=0.64. See link for more on morphometricity (and BLUP)
onlinelibrary.wiley.com
A unified framework for association and prediction from vertex‐wise grey‐matter structure
This manuscript introduces a set of analyses, that rely on linear mixed models to perform association and prediction, while being suited to tackle the challenges of big-data in neuroimaging. Our fram....
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
Our results highlight the difficulty to predict depression from structural brain MRI, which was previously reported in papers from the ENIGMA-MDD consortium.
nature.com
Classification of major depressive disorder using vertex-wise brain sulcal depth, curvature, and thickness with a deep and a shallow learning model - Molecular Psychiatry
Molecular Psychiatry - Classification of major depressive disorder using vertex-wise brain sulcal depth, curvature, and thickness with a deep and a shallow learning model
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
Interesting validation: our BLUP predictor was associated with a polygenic risk score for depression, but also captured additional information not currently tagged by the genetic predictor.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
Notably, the simple and efficient BLUP predictor outperformed the Deep Learning ResNet predictor, which is not unusual for brain-based predictors with these sample sizes.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
The main result is that brain-based predictors can do better than chance, but prediction remains low (OR=1.28; AUC=0.57), too low for clinical applications (e.g., aid diagnosis, referral).
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 25/02/2026
Happy to share our latest paper, the work of @clarajiang.bsky.social who trained brain-based predictors of depression on the UK Biobank (N=7,500 curated cases and matched controls) using AI/deeplearning as well as efficient statistical learning (BLUP). See thread below for a summary of findings
nature.com
Applying machine-learning and deep-learning to predict depression from brain MRI and identify depression-related brain biology - Translational Psychiatry
Translational Psychiatry - Applying machine-learning and deep-learning to predict depression from brain MRI and identify depression-related brain biology
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Reposted by Baptiste Couvy-Duchesne
Thomas Nichols @nichols.bsky.social · 19/02/2026
Save the date 👆🧵 Neuroimaging Statistics Workshop, 12-13 June, @ohbmofficial.bsky.social 2026 satellite meeting, w/ @ohbmossig.bsky.social's BrainHack. Keith Worsley lecture by Sir. John Aston, + great work at Neuro/Stats/ML/AI interface. Registration opens soon! sites.google.com/view/nsw2026
sites.google.com
NeuroStats2026
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
What other criteria should we use to benchmark processing? Elise also quantified the carbon footprint associated with computation in her PhD thesis.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
Still, we hope our results can help researchers make informed decisions when selecting a processing. And that it can encourage others to evaluate other image processing options (e.g., different software versions, non-default settings).
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
Many questions remain. Would we see the same results in other age groups (e.g., ABCD data) or in other databases (we used @ukbiobank.bsky.social)?
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
To make things even more complicated, it may also depend on the trait you are interested in. On average FSL VBM does a good job, but for some traits like Alzheimer's disease or maternal smoking, FreeSurfer may yield more significant associations.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
We also demonstrated that each processing step captures a unique signal. So we cannot claim that a single processing (among the ones we considered) is the best. Some are better, but none is perfect.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
Elise's results also confirm that the choices of processing have important consequences on the results, which contributes to the reproducibility crisis. See results below for the same individuals and same trait (maternal smoking around birth - associated regions vary depending on processing)
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
Results (in brief) show that FSL VBM performs very well, capturing the most signal (morphometricity), yielding performant predictors, maximising power to detect associated brain regions, and yielding replicable results. pubmed.ncbi.nlm.nih.gov/41163627/
pubmed.ncbi.nlm.nih.gov
Choice of Processing Pipelines for T1-Weighted Brain MRI Impacts Association and Prediction Analyses - PubMed
The growing availability of large neuroimaging datasets, such as the UK Biobank, provides new opportunities to improve robustness and reproducibility in brain imaging research. However, little is known about the extent to which MRI processing pipelines influence results. Using 39,655 T1-weighted MRI …
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/11/2025
I have always wondered if there is a best method/software to process T1w image (at a vertex/voxel wise level). Elise Delzant has some answers in her first published paper from her PhD. She compared FreeSurfer, CAT12 and FSL across several traits and analyses (association, prediction).
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 28/03/2025
Post-doc job offer with Sonia Shah in Brisbane, working in statistical genetics within a great lab and ecosystem. www.linkedin.com/jobs/view/41...
linkedin.com
The University of Queensland hiring Postdoctoral Research Fellow - Statistical Genomics in St Lucia, Queensland, Australia | LinkedIn
Posted 12:03:06 PM. Institute for Molecular BioscienceFull-time (100%), fixed-term position for up to 2 yearsBase…See this and similar jobs on LinkedIn.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 18/02/2025
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 17/02/2025
@institutducerveau.bsky.social
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
Lastly, we showed that the brain-based predictor of Alzheimer's could also predict early AD, mild cognitive impairment, cognition, tau levels or genetic risk. Our predictor is on par with some of the best ones that can predict progression to AD, which could help with early intervention
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
Interestingly, the brain regions associated with Alzheimer's, disease progression and cognition overlapped suggesting some of the same regions are implicated. Some regions stand out being associated with many traits.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
We systematically attempted to replicate the results also showed the identified regions could help predict disease, progression and cognition in independent samples.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
We have also estimated that there should be at least 5 times more regions that remain to be identified (difference between the morphometricity and variance currently explained by the identified regions). Even more data will be needed!
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
Even better with a GIF (showing the regions with reduced thickness associated with Alzheimer's across the left subcortical structures)! Made with our R package brainMapR. github.com/baptisteCD/b...
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
Our high-resolution approach makes it possible to identify sub-regions of the hippocampus (or of the amygdala) that are involved, which can orient research towards specific brain regions/networks or cell populations.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
This is the largest study of its kind in terms of the number of participants (>9,000 subjects from 10 clinical cohorts+ the UK Biobank), and we have identified 103 grey matter regions associated with Alzheimer's, including some in ‘known’ regions, such as the hippocampus.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 06/02/2025
Our latest paper is out! A well powered high resolution mapping of the grey-matter regions associated with Alzheimer's, progression to Alzheimer's disease, cognition and functioning. @drbreaky.bsky.social @barkhof.bsky.social @michelleklupton.bsky.social
onlinelibrary.wiley.com
Grey‐Matter Structure Markers of Alzheimer's Disease, Alzheimer's Conversion, Functioning and Cognition: A Meta‐Analysis Across 11 Cohorts
We meta-analysed results from 11 neuroimaging cohorts of elderly participants, to estimate the morphometricity (total association with brain measurements) of 17 traits of interest, and to identify th...
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
At this point, we do not know if the identified drugs or conditions directly cause neurodegenerative disorders or whether they are early symptoms of the disease or reflect more complex aetiology. However, the results could be useful for personalising and accelerating referrals to neurologists.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
Likewise for medical conditions, which are associated with future risk of neurodegenerative disorders.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
Here is a summary of the drug classes, whose frequency of use differs in individuals who are going to receive a neurodegenerative diagnosis within 5-10 years.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
We focused on associations that were consistent across the different countries - hence, they cannot be attributed to specific health systems, bias in the data or the type of medical records (primary, hospital).
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
Using medical records from Australia, France, the UK and Sweden, we identified several drug usage, conditions and biomarkers associated up to 10 years before diagnoses.
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Baptiste Couvy-Duchesne @baptistecd.bsky.social · 05/02/2025
Here is our latest publication (the first from our Lemerend consortium) that looks at early risk factors of neurodegenerative disorders. Thank you to all the authors, and in particular the fantastic team of analysts!
sciencedirect.com
Ten years preceding a diagnosis of neurodegenerative disease in Europe and Australia: medication use, health conditions, and biomarkers associated with Alzheimer's disease, Parkinson's disease, and am...
Many studies have investigated early predictors for Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Howev…
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