DICOM ↔ NIfTI conversion

Convert a DICOM series to NIfTI (or back) for neuroimaging and research pipelines.

Problem

Your DICOM series needs to be converted to NIfTI-1 format for neuroimaging analysis pipelines (FSL, SPM, AFNI) or AI model training. NIfTI is the standard format for volumetric brain imaging — it stores 3D/4D data with an affine transformation matrix that maps voxel coordinates to scanner space, which DICOM doesn’t natively provide in a single file.

Steps

1. Open the DICOM file (⌘O) containing the series to convert.

2. Click Export in the top bar, then select Export Series to NIfTI-1 from the dropdown.

3. The browser triggers a download of a .nii.gz (gzip-compressed NIfTI) file.

4. Verify the output by inspecting the downloaded file:

   • The NIfTI header is at least 348 bytes
   • The magic string at offset 344 is n+1\0 or ni1\0
   • The volume dimensions (dim[1..3]) are positive integers
   • The affine matrix (srow_x, srow_y, srow_z) contains the spatial transformation — at least one component is non-zero (the affine is never identity for real DICOM→NIfTI)

Result

The output is a .nii.gz with a valid NIfTI-1 header whose dimensions match the source series and whose affine maps voxels into the DICOM patient coordinate system. The pixel data is gzip-compressed for smaller storage and transfer.