Research
Research
Research
Research
Software
We develop software for image processing, curation, quality assurance, and analysis. All software relies upon an open development model and "glass box" design. Together, these tools help accelerate reproducible neuroscience at scale.
QSIPrep (Cieslak et al., Nature Methods 2021) is a complete BIDS-app for processing diffusion-weighted MRI (dMRI) data. QSIPrep is compatible with nearly any acquisition scheme, and provides both top-performing pre-processing and reconstruction methods. QSIPrep has thus far been used to succesfully preprocess over 430,000 dMRI scans thus far.
QSIPrep
53k+
# downloaded
53k+
as of
4/26/26
XCP-D (Mehta & Salo et al., Imaging Neuroscience 2024) provides post-processing for fMRI data that has been processed using fMRIPrep or HCP pipelines. Features include quality assurance, confound regression, and many derived measures including networks at multiple scales. XCP-D has thus far been used to succesfully post-process over 410,000 fMRI scans.
XCP-D
36k+
# downloaded
36k+
as of
4/26/26
QSIRecon (Cieslak et al., bioRxiv 2025) builds post-processing workflows that produce many of the biologically-interesting dMRI derivatives used for hypothesis testing. QSIRecon has thus far been used to succesfully postprocess over 300,000 dMRI scans to date.
QSIRecon
13k+
# downloaded
13k+
as of
4/26/26
ASLPrep (Adebimpe et al., Nature Methods 2022) is a suite of software pipelines that ensure the reproducible and generalizable processing of ASL MRI data and quantification of brain perfusion. QSIPrep has thus far been used to succesfully preprocess approximately 70,000 ASL scans thus far.
ASLPrep
12k+
# downloaded
12k+
as of
4/26/26
Curation of BIDS (CuBIDS; Covitz et al., Neuroimage 2022) is a sanity preserving workflow and software package that aids users in curating (checking and fixing) large, heterogeneous BIDS datasets.
CuBIDS
4k+
# downloaded
4k+
as of
10/27/25
ModelArray (Zhao et al., Imaging Neuroscience 2023) is an R package for memory-efficient statistical analysis of high-dimensional imaging features including fixels, voxels, ciftis, and beyond.
ModelArray
1k+
# downloaded
1k+
as of
10/27/25
The BIDS App Boostrap (BABS; Zhao et al., Imaging Neuroscience 2024) is a user-friendly and generalizable Python package for reproducible image processing at scale. By leveraging DataLad, BABS facilitates the reproducible application of BIDS Apps to large-scale datasets.
BABS
250+
# downloaded
250+
as of
10/27/25
Flywheel Tools (Tapera et al., Frontiers in Neuroinformatics 2021) includes suite of tools for curating and organizing data in the Flywheel imaging database.
Flywheel Tools
200+
# downloaded
200+
as of
10/27/25
Multi Scale Network Regression (MSNR; Xia et al., Human Brain Mapping 2020) is an R based tool to extract multivariate brain-phenotype relationships in complex, high-dimensional network settings.
MSNR
50+
# downloaded
50+
as of
10/27/25