[HTML][HTML] Open and reproducible neuroimaging: From study inception to publication

G Niso, R Botvinik-Nezer, S Appelhoff, A De La Vega… - NeuroImage, 2022 - Elsevier
Empirical observations of how labs conduct research indicate that the adoption rate of open
practices for transparent, reproducible, and collaborative science remains in its infancy. This …

Towards a biologically annotated brain connectome

V Bazinet, JY Hansen, B Misic - Nature reviews neuroscience, 2023 - nature.com
The brain is a network of interleaved neural circuits. In modern connectomics, brain
connectivity is typically encoded as a network of nodes and edges, abstracting away the rich …

[PDF][PDF] DataLad: distributed system for joint management of code, data, and their relationship

Y Halchenko, K Meyer, B Poldrack, D Solanky… - Journal of Open Source …, 2021 - par.nsf.gov
Summary Data Lad is a Python-based tool for the joint management of code, data, and their
relationship, built on top of a versatile system for data logistics (git-annex) and the most …

ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion

A Adebimpe, M Bertolero, S Dolui, M Cieslak… - Nature …, 2022 - nature.com
Arterial spin labeled (ASL) magnetic resonance imaging (MRI) is the primary method for
noninvasively measuring regional brain perfusion in humans. We introduce ASLPrep, a …

Time-dependent memory transformation in hippocampus and neocortex is semantic in nature

V Krenz, A Alink, T Sommer, B Roozendaal… - Nature …, 2023 - nature.com
Memories undergo a time-dependent neural reorganization, which is assumed to be
accompanied by a transformation from detailed to more gist-like memory. However, the …

The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging

C Paquola, J Royer, LB Lewis, C Lepage, T Glatard… - Elife, 2021 - elifesciences.org
Neuroimaging stands to benefit from emerging ultrahigh-resolution 3D histological atlases of
the human brain; the first of which is 'BigBrain'. Here, we review recent methodological …

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 …

ENIGMA HALFpipe: interactive, reproducible, and efficient analysis for resting‐state and task‐based fMRI data

L Waller, S Erk, E Pozzi, YJ Toenders… - Human Brain …, 2022 - Wiley Online Library
The reproducibility crisis in neuroimaging has led to an increased demand for standardized
data processing workflows. Within the ENIGMA consortium, we developed HALFpipe (H …

The integrity of dopaminergic and noradrenergic brain regions is associated with different aspects of late-life memory performance

MJ Dahl, SL Bachman, S Dutt, S Düzel, NC Bodammer… - Nature Aging, 2023 - nature.com
Abstract Changes in dopaminergic neuromodulation play a key role in adult memory
decline. Recent research has also implicated noradrenaline in shaping late-life memory …

Quality control in functional MRI studies with MRIQC and fMRIPrep

C Provins, E MacNicol, SH Seeley… - Frontiers in …, 2023 - frontiersin.org
The implementation of adequate quality assessment (QA) and quality control (QC) protocols
within the magnetic resonance imaging (MRI) research workflow is resource-and time …