DICOMs to NIfTIs

There are many tools that are used to convert neuroimaging data from the DICOM format into NIfTI format, however the tool that is typically used in the DCAN Lab is dcm2niix.

The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices). dcm2niix is also able to generate a BIDS JSON format sidecar which includes relevant information for brain scientists in a vendor agnostic and human readable form.

While dcm2niix can be run on its own we recommend running it through dcm2bids. This pip installable utility is a wrapper for dcm2niix that takes the NIfTI outputs and reformates them according to the BIDS naming scheme and folder structure. This allows users to quickly identify image types and enables compataibility with any BIDS app including our image processing pipelines. dcm2bids requires a configuration file to correctly label the NIfTI file according to its image acquisition protocol. See the dcm2bids tutorial for more information.