56 Open source projects that are alternatives of or similar to Mriqc

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

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 Imaging Data Structure (BIDS) Specification

normalize the intensity of several MR image contrasts with various routines

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

TE-dependent analysis of multi-echo fMRI

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

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

Deep Learning Toolkit for Medical Image Analysis

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.

Machine learning for NeuroImaging in Python

Workflows and interfaces for neuroimaging packages

The MATLAB toolbox for MEG, EEG and iEEG analysis

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.

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

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.

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

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

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…

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

Probabilistic Threshold-Free Cluster Enhancement of Neuroimages

Core methods and structures for neuroscience research in Julia.

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

Coordinate- and image-based meta-analysis in Python

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.

FSL-R Interface package

medical image visualization library and development toolkit

3D Visualization of Brain MRI

Neuroimaging in Julia

MATLAB / Octave tools for BIDS datasets

Multi-modal Image Registration And Connectivity anaLysis

BIDScoin converts your source-level neuroimaging data to BIDS

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network

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

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

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

Software platform for clinical neuroimaging studies

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

Utility functions for working with DICOM and BIDS neuroimaging data

MATLAB/Octave GIfTI Library

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

Method container for computational neuroscience on brains.

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

NeuroInformatics Database

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. 🤠

Graph theory analysis of brain MRI data

The NeuroMorph analysis and visualization toolkit

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

Code related to Neuroimaging Analysis Replication and Prediction Study

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

Brain Imaging Analysis Kit

Neuroimaging analysis and visualization suite