The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets

S Larivière, C Paquola, B Park, J Royer, Y Wang… - Nature …, 2021 - nature.com
Through harmonized procedures and by sharing site-specific brain metrics (for example,
cortical thickness) or aggregated statistical maps, ENIGMA has set the stage for large-scale …

[HTML][HTML] Neuromaps: structural and functional interpretation of brain maps

RD Markello, JY Hansen, ZQ Liu, V Bazinet, G Shafiei… - Nature …, 2022 - nature.com
Imaging technologies are increasingly used to generate high-resolution reference maps of
brain structure and function. Comparing experimentally generated maps to these reference …

[HTML][HTML] Micapipe: A pipeline for multimodal neuroimaging and connectome analysis

RR Cruces, J Royer, P Herholz, S Larivière… - NeuroImage, 2022 - Elsevier
Multimodal magnetic resonance imaging (MRI) has accelerated human neuroscience by
fostering the analysis of brain microstructure, geometry, function, and connectivity across …

[HTML][HTML] Predicting regional neurodegeneration from the healthy brain functional connectome

J Zhou, ED Gennatas, JH Kramer, BL Miller… - Neuron, 2012 - cell.com
Neurodegenerative diseases target large-scale neural networks. Four competing
mechanistic hypotheses have been proposed to explain network-based disease patterning …

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

AI Renton, TT Dao, T Johnstone, O Civier… - Nature …, 2024 - nature.com
Neuroimaging research requires purpose-built analysis software, which is challenging to
install and may produce different results across computing environments. The community …

[HTML][HTML] Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks

D Maric, J Jahanipour, XR Li, A Singh, A Mobiny… - Nature …, 2021 - nature.com
Mapping biological processes in brain tissues requires piecing together numerous
histological observations of multiple tissue samples. We present a direct method that …

A community-developed open-source computational ecosystem for big neuro data

JT Vogelstein, E Perlman, B Falk, A Baden… - Nature …, 2018 - nature.com
To the Editor—Recent technological developments, such as high-throughput imaging and
sequencing, enable experimentalists to collect increasingly large, complex, and …

Building better biomarkers: brain models in translational neuroimaging

CW Woo, LJ Chang, MA Lindquist, TD Wager - Nature neuroscience, 2017 - nature.com
Despite its great promise, neuroimaging has yet to substantially impact clinical practice and
public health. However, a developing synergy between emerging analysis techniques and …

[HTML][HTML] Inference in the age of big data: Future perspectives on neuroscience

D Bzdok, BTT Yeo - Neuroimage, 2017 - Elsevier
Neuroscience is undergoing faster changes than ever before. Over 100 years our field
qualitatively described and invasively manipulated single or few organisms to gain …

Moving beyond processing and analysis-related variation in neuroscience

X Li, NB Esper, L Ai, S Giavasis, H Jin, E Feczko, T Xu… - BioRxiv, 2021 - biorxiv.org
When fields lack consensus standards and ground truths for their analytic methods,
reproducibility can be more of an ideal than a reality. Such has been the case for functional …