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MRI data format

MRI Scanner Data Format

Every scanner manufacturer (Philips, Siemens, GE, etc.) have their own data format. Siemens data is stored in DICOM files that usually are transformed into a standardized image format developed by the Neuroimaging InFromatics Technology Initiative. Most programms and imaging packages can work with this NIFTI format thus converting the images is essential before analysis. Also BIDS works with NIFTI files.

DICOM (digital imaging and communications in medicine)

Is the format for most medical images. It is made up of two parts: a header and the actual image. The header contains data about the image such as demographic information, certain parameters, pixel intensity, matrix size, etc. Viewing data in DICOM format requires specified software, additionally the data cannot be opened directly anymore as soon as they have been compromised onto a drive.

NIFTI (Neuroimaging Informatics Technology Initiative)

Replacement for ANALYZE 7.5 file format, which did not contain information about orientation in space. ANALYZE 7.5 contained a header (.hdr) and and image (.img) file such as DICOM. The new NIFTI format includes the header and image into one single file. The NIFTI format stores data in multiple dimensions: 1. x-axis, 2. y-axis, 3. z-axis, 4. time, 5.-7. none. All images that end with .nii are nifti files and can be compressed into .nii.gz (gzip).

Further Data Formats

TSV

  • Tap-seperated Value

  • Most of the metadata are stored in this format

Json

  • A compact data format in a easy readable text form

  • Name stands for Javascript object notation

  • Is used for standardized meta data in a separate file

  • See „further links“