Code & data
Software, datasets, atlases, and standards
Everything here is open. Most of it runs on, or is distributed through, our cloud platform; the rest is on GitHub or in the journals’ data repositories. Lab code is at github.com/pestillilab, github.com/francopestilli, and github.com/brainlife.
Platforms and tools
brainlife.io
Open cloud platform that connects neuroimaging data, versioned apps, and outputs with full provenance; runs on cloud and HPC.
ezBIDS
Guided conversion of raw scanner data into the Brain Imaging Data Structure, interoperable with the major archives.
dicompare
Validates and compares MRI acquisition protocols from DICOM metadata, so that sessions from different sites and scanners can be checked against a reference or a shared schema. Python package and web app.
VISCONN
Toolbox for measuring white-matter connectivity between retinotopically matched regions of visual cortex; distributed as brainlife.io apps.
LiFE and ENCODE
Linear fascicle evaluation and the multidimensional encoding of connectomes, for evaluating and comparing tractography.
Datasets, atlases and benchmarks
White Matter Tract Termination Atlas (WMTTA)
Where 61 major tracts terminate on the cortical surface, from 1,062 Human Connectome Project participants, with functional profiles.
Tract segmentation generalizability benchmark
1,455 subjects across children, young adults, and aging adults with 61 labeled tracts, for testing deep-learning tract segmentation across datasets.
Center for Mesoscale Connectomics data
Macaque brains imaged at 10.5 T in vivo and ex vivo, with whole-brain PS-OCT and processing pipelines.
A taxonomy of the brain's white matter
Twenty-one major tracts defined and named for the 21st century, with reproducible segmentation.
Open diffusion data derivatives (O3D)
Upcycled diffusion MRI derivatives from public datasets, processed with integrated, reproducible pipelines.
A labeled clinical-MRI dataset of Nigerian brains
Clinical MRI scans from Nigeria, labeled and shared to broaden the populations represented in neuroimaging.
Standards and governance
BIDS Connectivity
The community extension of the Brain Imaging Data Structure for macroscopic brain connections and the workflows that produce them.
Neurodata governance toolkit
Legal map of 93 countries, decision tools, and a modular neurodata transfer and access agreement, from the BRIDGE program.
Teaching materials
Foundations of Psychological Data Science I
Full course as runnable Jupyter notebooks, from the Psychological Data Science organization at UT Austin. MIT license.
Foundations of Psychological Data Science II
The second semester of the course, also as open notebooks.