DICOM and NIfTI format

DICOM format

The images exported from an MRI scanner will be in DICOM format. It is the international standard format for medical images and related information.

Even if DICOM is a standard, there are a lot of differences between DICOM of each manufacturers (Philips, Siemens, GE...) and between the DICOM for each modality. Manufacturers publish DICOM conformance statement for each modality (for example here for Philips MRI).

DICOM file are composed of 2 parts:

  • the image data (sometime compressed)
  • the header that contains the metadata. In this part you can find tags fabout the scanner, the subject or the acquisitions parameters. Note that each manufacturer has private tags that are not necessarily specified in the standard.

For "Classic DICOM" files, there is a DICOM file for each slice of the volume.
You can also have "Enhanced DICOM" files and in this case, all the slices of the volume are stored in one DICOM file. The header is not structured in the same way for Enhanced and Classic DICOM.

Others Philips data

Philips also allows to export data in PAR/REC format (an ASCII header (PAR) plus a binary blob (REC)) or in XML/REC format. There are older formats contening less information than the DICOM format, and are therefore not recommended for use in new studies.

Conversion into NIfTI

The Neuroimaging Informatics Technology Initiative (NIfTI) is an open file format commonly used to store brain imaging data. This article summarizes information about this format. As the NIfTI format does not contain all the metadata, the NIfTI file is often paired with a file in json format that contains metadata information.

Conversion into NIfTI using dcm2niix

dcm2niix software can be used to convert data from the DICOM format to the NIfTI format (with a json file).

There are specificities for each manufacturer (for example image scaling or information in json file), for Philips data please see here.

Note that Philips DICOM do not contains some information as slice timing, phase encoding direction or total readout time (see here).

If you want to organize your data in BIDS format, please see here