Conversion Tools
dcm2niix
CLI
In my exploration of tools for BIDSification, I came across dcm2niix, which is a crucial piece of software written in C++. It is designed to convert DICOM and PAR/REC files into the NIfTI format, a key step in preparing data for BIDS compliance. It's specifically engineered to handle brain imaging data conversions with minimal fuss, making it a favorite among researchers and clinicians alike. The software automatically generates JSON sidecar files for each NIfTI file it creates, which include important metadata necessary for BIDS datasets.
Among all, dcm2niix stands out for its efficiency in converting DICOM and PAR/REC files into NIfTI format. Its speed, ease of use, and broad compatibility make it a preferred choice when it comes to big data.
BIDS-converter
MATLAB and Python
BIDS-converter facilitates the conversion of PET images from DICOM and ECAT formats to NIfTI, leveraging both Matlab and Python scripts. It supports a wide range of PET imaging data, making it versatile for research and clinical use.
Heudiconv
Python
Heudiconv is tailored for converting DICOM files to the NIFTI format within a BIDS structure. Its tools are especially useful at the initial stages of BIDSification, facilitating the conversion of raw imaging data into a structured, standardized format.
nipype
Python
Nipype can use dcm2niix to convert images, showcasing the tool's utility in facilitating neuroimaging workflows across various programming environments.
dcmstack
Python
Dcmstack is a Python-based tool that converts DICOM images to NIfTI format while preserving metadata. It's particularly useful for researchers who need to retain study-specific information within the imaging files.
dicom2nifti
Python
Dicom2nifti is a Python wrapper that utilizes the high-performance GDCMCONV executables for converting DICOM images to NIfTI. It's designed for efficiency and can handle a broad range of DICOM data.
dicm2nii
Matlab
This tool, developed in Matlab, allows for the scriptable conversion of DICOM images to NIfTI. Its Matlab foundation makes it highly adaptable for automated workflows and custom processing pipelines.
dicomtonifti
CLI
Dicomtonifti extends the capabilities of VTK, a widely used toolkit for 3D computer graphics, image processing, and visualization, to convert DICOM images to NIfTI format.
dinifti
CLI
Dinifti focuses on converting Siemens DICOM data to NIfTI, addressing the specific needs of researchers and clinicians working with Siemens imaging equipment.
DWIConvert
CLI and GUI
DWIConvert specializes in converting DICOM images to NRRD and NIfTI formats, making it a valuable tool for researchers working with diffusion-weighted imaging data.
mri_convert
CLI
This tool is integrated within the FreeSurfer suite, known for its robustness in processing GE and Siemens data, though it may encounter difficulties with Philips 4D datasets.
nanconvert
CLI
Nanconvert leverages the ITK library to convert DICOM images from GE and proprietary Bruker formats to standard formats like DICOM, addressing niche conversion needs.
Simple Dicom Reader 2 (Sdr2)
GUI
Simple Dicom Reader 2 utilizes dcmtk to read and convert DICOM images to the NIfTI format, providing a straightforward solution for DICOM processing.
spec2nii
Python
Spec2nii is tailored for converting MR spectroscopy data to NIfTI, addressing the specific needs of spectroscopy analysis in research and clinical settings.
bidskit
Python
Bidskit utilizes dcm2niix to create BIDS datasets, streamlining the process with detailed guidance for users new to BIDS or neuroimaging data management.
BIDScoin
GUI, Python and CLI
BIDScoin offers a user-friendly GUI for converting DICOM images to BIDS format. Its comprehensive documentation supports users through the conversion process.
conversion
Python
This Python library converts dcm2niix-created NIfTI files to the popular NRRD format, including DWI gradient tables. It highlights the versatility of dcm2niix in supporting various data formats.
DAC2BIDS
CLI
DAC2BIDS leverages dcm2niibatch to create BIDS datasets, providing an efficient path for researchers to organize their imaging data in line with BIDS standards.
dcm2bids
CLI
Dcm2Bids facilitates the creation of BIDS datasets using dcm2niix, supported by a comprehensive tutorial that guides users through the conversion process.
dcm2niir
R
Dcm2niir is an R wrapper for dcm2niix/dcm2nii, extending the accessibility of DICOM to NIfTI conversion to the R programming community.
dcm2niixpy
Python
Dcm2niixpy is a Python package of dcm2niix, offering Python users direct access to dcm2niix's functionalities within their programming environment.
dcm2niix_afni
CLI, Python
This version of dcm2niix is included with the AFNI distribution, integrating DICOM to NIfTI conversion within a comprehensive suite of tools for brain imaging analysis.
dcm2niiXL
CLI
Dcm2niiXL is a shell script and optimized compilation of dcm2niix designed for fast conversion of extra-large datasets, addressing the needs of high-throughput imaging studies. dcm2niiXL is a script for running dcm2niix in parallel.
heudiconv
CLI, Python
Heudiconv can use dcm2niix to create BIDS datasets, facilitating the conversion of data acquired using the reproin convention into organized, shareable, and version-controlled datasets.
MRIcroGL
GUI
Available for MacOS, Linux, and Windows, MRIcroGL provides a graphical interface for dcm2niix, facilitating the conversion of DICOM images in a user-friendly environment.
NeuroElf
GUI and MATLAB
NeuroElf can use dcm2niix to convert DICOM images, integrating this capability within its suite of tools for neuroimaging data analysis and visualization.
TractoR
R
TractoR (Tractography with R) uses dcm2niix for image conversion, integrating DICOM to NIfTI conversion within its suite of tools for advanced neuroimaging analyses and tractography with R.