64 Open source projects that are alternatives of or similar to fmriflows

MATLAB / Octave tools for BIDS datasets

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network

Graph theory analysis of brain MRI data

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.

BIDScoin converts your source-level neuroimaging data to BIDS

This repository contains the code of LiviaNET, a 3D fully convolutional neural network that was employed in our work: "3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study"

Brain extraction in presence of abnormalities, using single and multiple MRI modalities

TE-dependent analysis of multi-echo fMRI

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

Public release of The Cole-Anticevic Brain-wide Network Partition (CAB-NP)

normalize the intensity of several MR image contrasts with various routines

Code and data for Zhang, Lengersdorff et al. (2020)

A list of tutorials and other resources useful to learn open science and neuroimaging, EEG and MEG

The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠

Learn Nipype with these tutorial notebooks - go here to see them online -->

ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.

Slicer extensions index

Diffusion MRI analysis and visualization in 3D Slicer open source medical imaging platform.

Multi-platform, free open source software for visualization and image computing.

Workflows and interfaces for neuroimaging packages

The NeuroMorph analysis and visualization toolkit

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

Neuroimaging analysis and visualization suite

MATLAB/Octave GIfTI Library

A curated list of awesome deep learning applications in the field of neurological image analysis

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.

Brain Imaging Data Structure (BIDS) Specification

Method container for computational neuroscience on brains.

MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python

Neuroimaging in Julia

Easy and comprehensive assessment of predictive power, with support for neuroimaging features

NeuroInformatics Database

Deep Learning Toolkit for Medical Image Analysis

Framework for the reproducible processing of neuroimaging data with deep learning methods

A Deep Graph Neural Network Architecture for Modelling Spatio-temporal Dynamics in rs-fMRI Data

Multi-platform, free open source software for visualization and image computing.

medical image visualization library and development toolkit

The open source toolbox for reproducible diffusion MRI-based microstructure estimation

Machine learning for NeuroImaging in Python

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

The MATLAB toolbox for MEG, EEG and iEEG analysis

Software platform for clinical neuroimaging studies

Pycortex is a python-based toolkit for surface visualization of fMRI data

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

Multi-modal Image Registration And Connectivity anaLysis

Easylearn is designed for machine learning mainly in resting-state fMRI, radiomics and other fields (such as EEG). Easylearn is built on top of scikit-learn, pytorch and other packages. Easylearn can assist doctors and researchers who have limited coding experience to easily realize machine learning, e.g., (MR/CT/PET/EEG)imaging-marker- or other…

Code related to Neuroimaging Analysis Replication and Prediction Study

Core methods and structures for neuroscience research in Julia.

Probabilistic Threshold-Free Cluster Enhancement of Neuroimages

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

FSL-R Interface package

3D Visualization of Brain MRI

A framework for developing neural network models for 3D image processing.

Utility functions for working with DICOM and BIDS neuroimaging data

Brain Imaging Analysis Kit