DICOM TO NIFTI · BASIC · RESEARCH & EDUCATION
DICOM to NIfTI, without the command line.
OmniDICOM is a DICOM viewer for Mac and Windows that saves a series as NIfTI. Open the series, look through it, then choose File ▸ Export as NIfTI…: each series becomes one compressed NIfTI-1 file (.nii.gz) holding its original values (HU for CT), with its position and orientation in patient space, for the segmentation, registration and statistics tools that read NIfTI. It runs on your own computer and works in Basic, Professional and the 14-day trial.
No card required. After the trial, saving NIfTI needs a Basic or Professional subscription.
- A CT series
- File ▸ Export as NIfTI…
- NIfTI (volume), original values
- Exported 1 NIfTI volume
One .nii.gz per series
Compressed NIfTI-1, straight into your folder
Original values
HU for CT, after rescale slope and intercept
In patient space
Position and orientation, in millimetres
Based on OmniDICOM 1.1.4 · Application interface: English
How to convert a DICOM series to NIfTI
- Open the series in the viewer. Choose Open Folder… from the File menu, or drag the folder into the viewer. A study in the Local archive opens in the viewer with a double-click; NIfTI is saved from the viewer, not from the archive’s own Export. Wait until the series has finished loading.
- Choose File ▸ Export as NIfTI…. The Export dialog opens with NIfTI (volume) already chosen. You can also open File ▸ Export… and choose NIfTI (volume) as the format.
- Choose the series. Current series saves the series in the active panel, Selected series the series selected in the list, and All opened series every series loaded. Current image is greyed out, because a NIfTI file always holds a whole series.
- Check the values and the folder. Click More options. Values is Original values (HU for CT), the default. Under Export location, set the Folder, or Export asks for one. Image size, annotations, quality and frame rate are hidden: nothing of the display goes into the file.
- Resample only if a slice is missing. A series whose slices are not evenly spaced is not exported unless you tick Resample to even spacing. The missing slices are then filled in by linear interpolation, and the file name ends in _resampled.
- Export and read the result. Click Export. When every series was saved, the status bar says, for example, “Exported 3 NIfTI volumes.” Otherwise an Export finished dialog gives the counts and the reasons, up to five lines.
What the NIfTI file holds
| Format | NIfTI-1, one compressed file per series (.nii.gz), written straight into the export folder. No sidecar file is written. |
|---|---|
| Values | The original values after rescale slope and intercept: Hounsfield units for CT, the scanner’s own units for MR, and for PET the units in the file, often Bq/mL (not SUV). When every slice has the same rescale, the stored integers with the slope and intercept in the header; otherwise floating-point values. |
| Position | The orientation matrix (qform and sform, both “scanner”) places every voxel in patient space, converted from DICOM to the RAS convention other tools expect, so they show the anatomy the right way round. Slices are ordered from the lowest position along the slice normal. |
| Units | Millimetres |
| Not applied | Window, inversion, filters, rotation, flip, crop, fusion and measurements |
| File name | Like the movie exports (S3_….nii.gz), ending in _resampled when that applies and in _2 when another volume already has the name. An earlier export of the same series to the same folder is replaced. |
| Description | OmniDICOM, its version, the modality and “original values” |
The values are read from the files themselves, not from the screen, so a long thin-slice series is exported whole. On Professional, and during the trial, Values also offers Denoised values (HU for CT) once Denoise has finished every slice of a series; those files end in _denoised.
Which series can be saved
Original series of 3 or more parallel slices can be saved, and so can volumes made with Split series. A series that holds several volumes, such as several phases or echoes, must be split first: Split series is under Layout in the toolbar. When the scope holds no such series, the format is greyed out with the tooltip “NIfTI needs an original series of 3 or more parallel slices”.
These are not saved:
- MPR planes, 3D views and other results computed in the viewer
- Colour images: NIfTI export is for grayscale volumes
- CT acquired with a tilted gantry
- Images with no position or orientation tags, such as X-ray or ultrasound images, or with no pixel spacing
- Series that mix image sizes, or whose slices do not line up into one stack
- In this version: RT dose grids, and multi-frame files that give one position for all their frames, such as nuclear medicine files
A series that cannot be saved is left out with one line saying why, and the rest are still saved. Series with fewer than 3 images are left out without counting as failures.
A NIfTI file is not de-identified
A NIfTI file carries no patient name or ID, but it is not de-identified: a head scan can be reconstructed into a face, and the file name holds the end of the series identifier. To prepare a dataset, make a de-identified copy in the Local archive first, open the copy, then export it as NIfTI. De-identify DICOM studies →
What you need
- Basic, Professional or the 14-day trial. Every computer starts with 14 days of Professional, no card required. After the trial, or once a subscription has lapsed, Export as NIfTI — Needs a subscription opens instead, and nothing is written.
- An original series of 3 or more parallel slices, with position, orientation and pixel spacing in its DICOM tags.
- Mac: Apple silicon and macOS 13 or later. Windows: 64-bit Windows 10 or 11. The same menu and the same dialog on both.
- An internet connection to start the trial and for licensing and update checks. The volume is written on your computer; nothing is uploaded.
Common questions
Does the NIfTI file keep Hounsfield units?
Yes. A CT series is saved in Hounsfield units, after rescale slope and intercept. MR keeps the scanner’s own units, and PET the units in the file, often Bq/mL (not SUV).
Will other tools show the right orientation?
Yes. The orientation matrix (qform and sform, both “scanner”) places every voxel in patient space in millimetres, in the RAS convention other tools expect, so they show the anatomy the right way round.
Why is NIfTI greyed out?
The chosen scope holds no original series of 3 or more parallel slices. Choose another scope or series. A series that holds several volumes, such as phases or echoes, must be split first with Split series.
What if a slice is missing?
A series with uneven slice spacing is not exported unless you tick Resample to even spacing. Then it is resampled onto an even grid at the spacing it was acquired with, the missing slices are filled in by linear interpolation, and the file name ends in _resampled.
Is the NIfTI file de-identified?
No. It carries no patient name or ID, but a head scan can be reconstructed into a face, and the file name holds the end of the series identifier. De-identify a copy first if the data will be shared.
Can I save NIfTI during the 14-day trial?
Yes. NIfTI saving works in Basic, Professional and the 14-day trial. After the trial it needs a Basic or Professional subscription; Basic is US$10 a month or US$99 a year per computer.
Does it replace a command-line converter such as dcm2niix?
Not for every job. For converting many studies in a script, or when you need BIDS sidecar files, a command-line converter such as dcm2niix, the widely used open-source converter by Chris Rorden, fits better. OmniDICOM saves one .nii.gz per series from the viewer, after you have looked through the series, and writes no sidecar file.
Can I use it for diagnosis?
No. OmniDICOM is for research and education only. It is not a medical device and is not intended for diagnosis or clinical decision-making.
TRY IT ON YOUR OWN SERIES
Try NIfTI export for 14 days.
The download needs no card. The 14-day Professional trial starts on first launch with an internet connection, and De-identify and NIfTI saving work in it. After the trial, Basic, which includes both, is US$10 a month per computer. Pictures and movies exported during the trial carry a watermark; de-identified copies and NIfTI volumes do not.
OmniDICOM runs on Mac and Windows computers. Open this page on your computer to download it. Meanwhile, read the how-to guides or watch OmniDICOM at work on YouTube.
macOS 13+ · Apple silicon · signed, notarized PKG
Windows 10/11 · 64-bit · signed EXE
More about NIfTI export
Image credits
The clip is a capture of the OmniDICOM app with patient data hidden; the pointer is drawn in and waits are cut. The study is a public CT study, copied and given a demo identity for the capture. LDCT-and-Projection-data: McCollough C, et al. (2020), The Cancer Imaging Archive, doi:10.7937/9npb-2637, CC BY 4.0, modified; NIBIB grants EB017095 and EB017185.