Welcome to the weekly Jounal Club, where relevant articles and tools are presented by the Neuro-iX lab !
Presentation of the article: Contrast input and manual interventions significantly affect FreeSurfer morphometry and clinical correlations
neuroimage pipeline
freesurfer
contrast image
cortical surface reconstruction
Presentation of the article: The Developing Human Connectome Project: A fast deep learning-based pipeline for neonatal cortical surface reconstruction
neuroimage pipeline
deep learning
neonatal brain mri
cortical surface reconstruction
Presentation of the tool MedAbstain
llm
uncertainty bench
clinical uncertainty
Presentation of his paper: Automatic Landmark‑Based Segmentation of Human Subcortical Structures in MRI
landmark-based segmenation
atlas
deep learning
Presentation of Transductive Zero-Shot & Few-Shot Adaptation of Large Medical Vision Language Models
computer vision
language change
machine translation
machine learning
ophthalmology
predictive medicine
Presentation of the article: Assessing the impact of virtual reality on surgeons’ mental models of complex congenital heart cases
cyberpsychology
medical education
virtual and augmented reality
Presentation of MIMM-X: Disentangling Spurious Correlations for Medical Image Analysis
multiple spurious correlations
mri
ct scan
deep learning
Presentation of TRUST: Test-Time Refinement using Uncertainty-Guided SSM Traverses
state space model
vmamba
distribution shift
test-time adaptation
Presentation of SimCortex: Collision-Free Simultaneous Cortical Surfaces Reconstruction
cortical surface reconstruction
brain segmentation
geometric deep learning
brain MRI
3d deep learning
Presentation of NeuroBOLT: Resting-state EEG-to-fMRI synthesis with multi-dimensional feature mapping
transformer
image modality translation
fmri
eeg
Presentation of the article ‘DDM^2: Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models’
generative model
denoising
diffusion mri
Presentation of the article ‘Towards user-centered interactive medical image segmentation in VR with an assistive AI agent’
vr
ai agent
interactive segmentation
Presentation of several management and computing tools
tools
python librairies
Presentation of MedVQA: a Vision–Language Model for Visual Question Answering in Medical Imagery
computational vision & language
medical visual question answering
transformers & attention models
Presentation of the DeepPrep: an accelerated, scalable and robust pipeline for neuroimaging preprocessing empowered by deep learning
container
neuroimaging pipeline
study design & methodology & scalability
workflow management & platforms
Presentation of the article ‘A VR-based volumetric medical image segmentation and visualization system with natural human interaction’
natural user interface-enabled volume rendering system
virtual reality
Ten articles about automatic Landmark Detection
automatic landmark detection
cnns & fully convolutional networks
Conditional Temporal Attention Networks for Neonatal Cortical Surface Reconstruction
cortical surface reconstruction
diffeomorphic neonatal
mri techniques & modalities
Nested Hierarchical Transformer: Towards Accurate, Data-Efficient and Interpretable Visual Understanding
functional & nested atlases
medical image segmentation
vision transformers
Presentation of the accepted article ‘Improving quality control of mri images using synthetic motion data’
general deep learning
mri techniques & modalities
quality assurance & control
Presentation of the article ‘3D Reconstructions of Brain from MRI Scans Using Neural Radiance Fields’
mri techniques & modalities
neural radiance & view synthesis
structure-from-motion & volumetric modeling
Presentation of FastSurfer LIT
brain segmentation
deep learning framework
disease-focused imaging
image synthesis & inpainting
Presentation of Pytorch Lightning
deep learning framework
programming libraries & frameworks
Presentation of the review article ‘Addressing fairness issues in deep learning-based medical image analysis: a systematic review’
3d medical imaging
ethics & fairness & societal impact
general deep learning
Presentation of MONAI Label
3d medical imaging
few-shot & active learning
general deep learning
interactive segmentation methods
Presentation of the article ‘Green AI’
computational vision & language
ethics & fairness & societal impact
machine learning
study design & methodology & scalability
Presentation of the article ‘Semi-supervised few-shot learning for medical image segmentation’
few-shot & active learning
medical image segmentation
unlabeled surrogate tasks
Presentation of the review article ‘EPI susceptibility correction introduces significant differences far from local areas of high distortion’
diffusion imaging & features
echo planar imaging & artifacts
preprocessing & data sampling
quality assurance & control
Presentation of the review article ‘Automated brain segmentation and volumetry in dementia diagnostics: a narrative review with emphasis on FreeSurfer’
brain segmentation
disease-focused imaging
freesurfer & ecosystem tools
mri techniques & modalities
volumetry
Presentation of the article ‘Multi-Atlas Segmentation with Joint Label Fusion’
atlas-based methods & fusion
medical image segmentation
mri techniques & modalities
Presentation of the online platform brainlife.io
calibration & standardization
mri techniques & modalities
neuroimaging
workflow management & platforms
Presentation of SimpleClick
interactive segmentation methods
masked autoencoder
vision transformers
Presentation of the MITB functional atlas of the cerebral cortex
cortex parcellation
functional & nested atlases
mri techniques & modalities
Presentation of FET-MRQC
developmental brain imaging
mri techniques & modalities
quality assurance & control
Presentation of the article ‘Neural deformation fields for template-based reconstruction of cortical surfaces from MRI’
brain segmentation
cortical surface reconstruction
geometric deep learning
mri techniques & modalities
registration techniques
Presentation of the article ‘Semi-automatic segmentation of the fetal brain from magnetic resonance imaging’
developmental brain imaging
mri techniques & modalities
registration techniques
structure-from-motion & volumetric modeling
Presentation of the FD-NET
echo planar imaging & artifacts
general deep learning
unsupervised learning
Presentation of the python library TorchIO
3d medical imaging
open-source
preprocessing & data sampling
programming libraries & frameworks
Presentation of the article ‘Robust T-Loss for Medical Image Segmentation’
label quality & robustness
medical image segmentation
Presentation of the conference paper ‘Learning Invariant Representations with a Nonparametric Nadaraya-Watson Head’
diffusion imaging & features
machine learning
nonparametric invariant representation
Presentation of FastSurferVINN
brain segmentation
mri techniques & modalities
resolution & distortion correction
Presentation of NeRF
3d medical imaging
image-based rendering
neural radiance & view synthesis
structure-from-motion & volumetric modeling
volume rendering
Presentation of Comet
machine learning
supervised learning
workflow management & platforms
Presentation of Synb0-DisCo
diffusion imaging & features
echo planar imaging & artifacts
generative models
image synthesis & inpainting
Presentation of the article ‘Boundary-weighted logit consistency improves calibration of segmentation networks’
calibration & standardization
consistency regularization techniques
medical image segmentation
Presentation of Vox2Cortex
cortical surface reconstruction
geometric deep learning
mri techniques & modalities
Presentation of DARQ
general deep learning
quality assurance & control
registration techniques
Presentation of the review article ‘Best Practices in Structural Neuroimaging of Neurodevelopmental Disorders’
developmental brain imaging
freesurfer & ecosystem tools
mri techniques & modalities
neurodevelopmental disorders
quality assurance & control
study design & methodology & scalability
Presentation of the article ‘Disentangling Human Error from the Ground Truth in Segmentation of Medical Images’
cnns & fully convolutional networks
medical image segmentation
supervised learning
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