BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

A Model of Representational Spaces in Human Cortex

(2016) J. Swaroop Guntupalli et al.   CEREBRAL CORTEX

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments

(2016) Krzysztof J. Gorgolewski et al.   Scientific Data

A purely confirmatory replication study of structural brain-behavior correlations

(2015) Wouter Boekel et al.   CORTEX

Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres

(2015) David A. Raffelt et al.   NEUROIMAGE

The effects of SIFT on the reproducibility and biological accuracy of the structural connectome

(2015) Robert E. Smith et al.   NEUROIMAGE

An Automated, Adaptive Framework for Optimizing Preprocessing Pipelines in Task-Based Functional MRI

(2015) Nathan W. Churchill et al.   PLoS One

The Preprocessed Connectomes Project Quality Assessment Protocol - a resource for measuring the quality of MRI data.

(2015) Shehzad Zarrar et al.   Frontiers in Neuroscience

The impact of Docker containers on the performance of genomic pipelines

(2015) Paolo Di Tommaso et al.   PeerJ

Bioboxes: standardised containers for interchangeable bioinformatics software

(2015) Peter Belmann et al.   GigaScience

Striatal shape abnormalities as novel neurodevelopmental endophenotypes in schizophrenia: A longitudinal study

(2014) M. Mallar Chakravarty et al.   HUMAN BRAIN MAPPING

Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates

(2014) Min Tae M. Park et al.   NEUROIMAGE

Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates

(2014) Jon Pipitone et al.   NEUROIMAGE

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

(2014) Anders Eklund et al.   Frontiers in Neuroinformatics

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

(2014) Tarek Sherif et al.   Frontiers in Neuroinformatics

Machine learning for neuroimaging with scikit-learn

(2014) Alexandre Abraham et al.   Frontiers in Neuroinformatics

The minimal preprocessing pipelines for the Human Connectome Project

(2013) Matthew F. Glasser et al.   NEUROIMAGE

A test-retest fMRI dataset for motor, language and spatial attention functions

(2013) Krzysztof J Gorgolewski et al.   GigaScience

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

(2012) Konstantinos Krampis et al.   BMC BIOINFORMATICS

Performing label-fusion-based segmentation using multiple automatically generated templates

(2012) M. Mallar Chakravarty et al.   HUMAN BRAIN MAPPING

Within-subject template estimation for unbiased longitudinal image analysis

(2012) Martin Reuter et al.   NEUROIMAGE

FreeSurfer

(2012) Bruce Fischl   NEUROIMAGE

Optimizing Preprocessing and Analysis Pipelines for Single-Subject fMRI: 2. Interactions with ICA, PCA, Task Contrast and Inter-Subject Heterogeneity

(2012) Nathan W. Churchill et al.   PLoS One

The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

(2012) Ed H. B. M. Gronenschild et al.   PLoS One

Open is Not Enough. Let's Take the Next Step: An Integrated, Community-Driven Computing Platform for Neuroscience

(2012) Yaroslav O. Halchenko et al.   Frontiers in Neuroinformatics

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows

(2012) Pierre Bellec et al.   Frontiers in Neuroinformatics

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Optimizing preprocessing and analysis pipelines for single-subject fMRI. I. Standard temporal motion and physiological noise correction methods

(2011) Nathan W. Churchill et al.   HUMAN BRAIN MAPPING

Neuroscience Runs on GNU/Linux

(2011) Michael Hanke et al.   Frontiers in Neuroinformatics

Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy

(2011) Anastasia Yendiki   Frontiers in Neuroinformatics

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

(2011) Krzysztof Gorgolewski et al.   Frontiers in Neuroinformatics

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Provenance in neuroimaging

(2008) Allan J. MacKenzie-Graham et al.   NEUROIMAGE