Comperhensive Tools

MRtrix

CLI

MRtrix3 provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI.

Plastimatch serves as a "Swiss Army knife" in image processing, offering features like registration, statistics, and a basic DICOM to NIfTI/NRRD image converter, making it highly versatile for medical imaging tasks.

pyBIDS

Python

pyBIDS is a cornerstone in the BIDS ecosystem, providing a suite of tools for querying, summarizing, and manipulating BIDS datasets. It acts as a bridge between BIDS datasets and Python-based neuroimaging software, enabling seamless integration and manipulation of data. Its flexibility and comprehensive nature make it an essential tool for researchers working with BIDS data.

bids-validator

Python

The bids-validator is crucial for ensuring datasets adhere to BIDS specifications. Although it's developed in JavaScript, it can be used alongside Python tools to validate datasets. This step is vital for verifying the correctness of the BIDS structure, especially before dataset sharing or analysis.

nibabel

Python

nibabel offers robust support for reading and writing various neuroimaging file formats. It's instrumental in the preprocessing stage, allowing researchers to manipulate neuroimaging data efficiently. Its capability to handle a wide range of formats makes it a versatile tool in the neuroimaging toolkit.

bidsify

Python

Bidsify is a Python project that employs dcm2niix to convert DICOM and Philips PAR/REC images to the BIDS standard, enhancing the accessibility and organization of neuroimaging data.

SPM12

MATLAB and CLI

SPM12 is a prominent tool in neuroimaging that includes DICOM to NIfTI conversion capabilities. Its Matlab basis allows for easy scripting and customization for various research needs.

BIDS Toolbox

Web Service

BIDS Toolbox is a web service designed for creating and manipulating BIDS datasets. It uses dcm2niix for importing DICOM data, providing an online solution for BIDS dataset management.

Banana

Python

Banana comprises a collection of brain imaging analysis workflows. It leverages dcm2niix for format conversions, facilitating comprehensive neuroimaging analyses.

BraTS-Preprocessor

GUI

This tool uses dcm2niix to import files for Brain Tumor Segmentation challenges. It exemplifies the application of standardized data in specialized research areas.

BioImage Suite Web Project

GUI, JavaScript

This JavaScript project incorporates dcm2niix in its DICOM conversion module, demonstrating the flexibility of dcm2niix across programming languages and platforms.

clinica

CLI

Clinica is a software platform tailored for clinical neuroimaging studies. It employs dcm2niix for converting DICOM images, supporting a wide range of neuroimaging analyses.

divest

R

Divest offers an R interface to dcm2niix, allowing R users to directly convert DICOM images within their analytical workflows.

ExploreASL

MATLAB

ExploreASL utilizes dcm2niix for importing images, supporting advanced analyses of arterial spin labeling (ASL) data and other perfusion MRI techniques.

ezBIDS

Web Service

EzBIDS is a web service that converts a directory full of DICOM images into BIDS format without requiring users to learn Python or any custom configuration, simplifying the BIDS conversion process.

fmrif tools

CLI

Fmrif tools use dcm2niix for its oxy2bids tool, part of a suite designed to facilitate the processing and analysis of functional MRI data.

LEAD-DBS

GUI

LEAD-DBS uses dcm2niix for DICOM import, supporting the planning and analysis of deep brain stimulation procedures with advanced imaging data.

Neuroinformatics Database (NiDB)

GUI Database

NiDB is designed for storing, retrieving, analyzing, and sharing neuroimaging data. It uses dcm2niix for image QA and handling some formats, demonstrating the utility of DICOM conversion in data management platforms.

shimming-toolbox

Python and CLI

Shimming-toolbox enables static and real-time shimming, using dcm2niix to import DICOM data. It supports the optimization of magnetic field homogeneity in MRI scans.

TORTOISE

CLI

TORTOISE is used for processing diffusion MRI data, employing dcm2niix for importing DICOM images. It underscores the tool's importance in diffusion imaging analyses.