TE-dependent analysis of multi-echo fMRI with tedana
TE-dependent analysis of multi-echo fMRI with tedana - Published in JOSS (2021)
fRAT
fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data - Published in JOSS (2023)
Connectome Mapper 3
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)
pycortex
Pycortex is a python-based toolkit for surface visualization of fMRI data
phys2cvr
python module to compute cerebrovascular reactivity mapping and other related maps
fmriprep
fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
nibabies
fMRIPrep Lifespan - A robust, transparent workflow tailored for neonate and infant MRI
csg_mri_pipelines
MRI preprocessing and analysis pipelines and tools for the study of disorders of consciousness
https://github.com/csinva/interpretable-embeddings
Interpretable text embeddings by asking LLMs yes/no questions (NeurIPS 2024)
pynets
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning
phys2denoise
A toolbox and collection of scripts to prepare physiology data for fMRI denoise
visualqc
VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.
https://github.com/bids-apps/rshrf
Resting state HRF estimation from BOLD-fMRI signal
simultaneous-fmri-and-eyetracking
Project repository for our first study on observing program comprehension with simultaneous fMRI and eye tracking
https://github.com/computationalpsychiatry/regressiondynamiccausalmodeling.jl
A Julia package for estimating directed connectivity in whole-brain networks
https://github.com/john-veillette/niseq
group sequential tests for neuroimaging
https://github.com/alfa-group/neural-program-comprehension
[eLife 2020] "Comprehension of computer code relies primarily on domain-general executive brain regions" by Anna A. Ivanova, Shashank Srikant, Yotaro Sueoka, Hope H. Kean, Riva Dhamala, Una-May O'Reilly, Marina U. Bers, Evelina Fedorenko
neuroim2
R data structures and function for fMRI-focused neuroimaging analysis
SPM 25
SPM 25: open source neuroimaging analysis software - Published in JOSS (2025)
https://github.com/csinva/total-variation-abide
Experiments with using total variation regularization on the ABIDE fmri dataset.
caton-pcb
Hardware design files for wireless EEG system used in concurrent TMS-EEG-fMRI
cpp_ptb
a set of function to make it easier to create behavioral, EEG, fMRI experiment with psychtoolbox
fmripost-rapidtide
A BIDS App for running rapidtide on a preprocessed fMRI dataset.
fmriflows
fmriflows is a consortium of many (dependent) fMRI analysis pipelines, including anatomical and functional pre-processing, univariate 1st and 2nd-level analysis, as well as multivariate pattern analysis.
halfpipe
ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data
https://github.com/brain-to/capsnet
Deep fMRI Encoding Models of Human Vision using Capsule Networks
https://github.com/brains-on-code/paper-esec-fse-2017
Measuring Neural Efficiency of Program Comprehension. Preprint of our paper:
automated-brain-explanations
Generating and validating natural-language explanations for the brain.
NeuroCAPs
NeuroCAPs: A Python Package for Performing Co-Activation Patterns Analyses on Resting-State and Task-Based fMRI Data - Published in JOSS (2025)
ddmra
Code for running distance-dependent motion-related artifact analyses in Python
https://github.com/codingfisch/niftiview-app
Standalone app for viewing volumetric images 🧠 based on Python
network_tda_tutorial
This repository is dedicated for the tutorial on network and topological neuroscience.
eCobidas
Working repository to turn the COBIDAS guidelines to report methods and results in neuroimaging into a user friendly checklist
fmri_processing_scripts
legacy signal processing leveraging afni, ants, fsl, nipy, robex, and wavelet toolbox - brnfswdktm