MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

JD Tournier, R Smith, D Raffelt, R Tabbara… - Neuroimage, 2019 - Elsevier
MRtrix3 is an open-source, cross-platform software package for medical image processing,
analysis and visualisation, with a particular emphasis on the investigation of the brain using …

Machine learning for precision psychiatry: opportunities and challenges

D Bzdok, A Meyer-Lindenberg - Biological Psychiatry: Cognitive …, 2018 - Elsevier
The nature of mental illness remains a conundrum. Traditional disease categories are
increasingly suspected to misrepresent the causes underlying mental disturbance. Yet …

The OpenNeuro resource for sharing of neuroscience data

CJ Markiewicz, KJ Gorgolewski, F Feingold, R Blair… - Elife, 2021 - elifesciences.org
The sharing of research data is essential to ensure reproducibility and maximize the impact
of public investments in scientific research. Here, we describe OpenNeuro, a BRAIN …

fMRIPrep: a robust preprocessing pipeline for functional MRI

O Esteban, CJ Markiewicz, RW Blair, CA Moodie… - Nature …, 2019 - nature.com
Preprocessing of functional magnetic resonance imaging (fMRI) involves numerous steps to
clean and standardize the data before statistical analysis. Generally, researchers create ad …

Open science challenges, benefits and tips in early career and beyond

C Allen, DMA Mehler - PLoS biology, 2019 - journals.plos.org
The movement towards open science is a consequence of seemingly pervasive failures to
replicate previous research. This transition comes with great benefits but also significant …

Singularity: Scientific containers for mobility of compute

GM Kurtzer, V Sochat, MW Bauer - PloS one, 2017 - journals.plos.org
Here we present Singularity, software developed to bring containers and reproducibility to
scientific computing. Using Singularity containers, developers can work in reproducible …

[HTML][HTML] Optical imaging and spectroscopy for the study of the human brain: status report

H Ayaz, WB Baker, G Blaney, DA Boas… - …, 2022 - spiedigitallibrary.org
This report is the second part of a comprehensive two-part series aimed at reviewing an
extensive and diverse toolkit of novel methods to explore brain health and function. While …

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites

O Esteban, D Birman, M Schaer, OO Koyejo… - PloS one, 2017 - journals.plos.org
Quality control of MRI is essential for excluding problematic acquisitions and avoiding bias
in subsequent image processing and analysis. Visual inspection is subjective and …

Extending the Human Connectome Project across ages: Imaging protocols for the Lifespan Development and Aging projects

MP Harms, LH Somerville, BM Ances, J Andersson… - Neuroimage, 2018 - Elsevier
Abstract The Human Connectome Projects in Development (HCP-D) and Aging (HCP-A) are
two large-scale brain imaging studies that will extend the recently completed HCP Young …

QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data

M Cieslak, PA Cook, X He, FC Yeh, T Dhollander… - Nature …, 2021 - nature.com
Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for
noninvasively studying the organization of white matter in the human brain. Here we …