io_nii2dcm

Convert NIfTI files to DICOM format.

Keywords : NIfTI, DICOM, Conversion

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Inputs

Input 1

Format : tuple val(meta), val(niftis), path(dicom)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
niftis	list	NIfTI files to be converted to DICOM format	True	*.{nii,nii.gz}
dicom	file	Reference DICOM file (optional)	True	*.dcm

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Outputs

dicom_directory

Format : tuple val(meta), path(DICOM/)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
DICOM/	directory	Directory containing the DICOM files	True	DICOM/

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
study_description	string	Study description to be added to the DICOM metadata (optional)	“
reference_dicom	file	Reference DICOM file to copy metadata from (optional)	“
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False
mrtrix_rng_seed	integer	Random seed for MRtrix3. Setting a fixed seed can help with reproducibility of results.	1234

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Tools

	Description	DOI
MRtrix3	MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging.	10.1016/j.neuroimage.2019.116137
nii2dcm	A tool to convert NIfTI files to DICOM format.

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Authors

• @GuillaumeTh

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Last updated : 2026-05-12