Why convert DCM to NIFTI?
DICOM stores each MRI or CT slice as a separate .dcm file, while neuroimaging analysis tools such as FSL, SPM, FreeSurfer, and ANTs expect a single NIfTI volume per scan. Converting packs the entire 3D series into one .nii or .nii.gz file, simplifying pipeline management and making the data immediately usable for brain segmentation, fMRI analysis, and voxel-based morphometry.
How to convert DCM to NIFTI
dcm2niix OPEN-SOURCE
Run dcm2niix -o /output -f %p_%s /dicom_folder in a terminal; it sorts slices, writes one .nii.gz per series, and produces a BIDS-compatible JSON sidecar automatically.
3D Slicer OPEN-SOURCE
Import the DICOM series via the DICOM module, load the desired series, then use File > Save and select the NIfTI .nii.gz format.
MRIcroGL FREE
Go to Import > Convert DICOM to NIfTI, select the input DICOM folder and output folder, then click Convert - MRIcroGL runs dcm2niix internally.
About these formats
.DCM
DICOM Medical Image
A DCM file is a DICOM medical image - an X-ray, CT, MRI, ultrasound, or mammogram - bundled together with patient and study information. To open it, use a free DICOM viewer: MicroDicom on…
Open .DCM details →A .NIFTI file is a data file used by specific software.
Open .NIFTI details →Quality & what to watch
- dcm2niix automatically processes multiple series in one folder and names each output file separately - no manual sorting is required.
- For uncompressed NIfTI output instead of
.nii.gz, add-z nto the dcm2niix command. - Verify orientation and coverage of the output volume in FSLeyes or MRIcroGL before passing it to an analysis pipeline.
Frequently asked questions
Why is NIfTI preferred over DICOM for neuroimaging research?
.dcm slices; every major neuroimaging tool reads it natively.
