Converting and Saving Siemens Mosaic Images

nordicICE can convert DICOM images in the Siemens Mosaic format to Nifti. The Mosaic format is unique to Siemens and is used to increase transfer efficiency (probably) by stacking multiple slices in a 3D volume into a single Dicom file as shown below:

Siemens Mosaic image format

Most versions of the Siemens Mosaic format are identified automatically from the Dicom header (but see note below). Several of the analysis modules in nordicICE (BOLD, DTI and ASL modules) automatically converts mosaic images during the pre-processing. It is also possible to manually convert Mosaic images to a flat format.

If the loaded image is recognized as a mosaic image, the option: Split mosaic will appear on the popup menu activated by right-clicking the mouse inside the image and the following dialog will appear:

The Siemens Mosaic format descriptor dialog

This dialog gives the details of the Mosaic image(s), as recognized by nordicICE. The data given here should be correct, by default, for all mosaic image types. The dialog is presented so that the format determined by nordicICE can be overridden by the user. In the example above, the mosaic image contains 5 rows and 5 columns and 20 slices with slice order descending (feet-head). Note that Images used can be less than Row x Cols, but never more.

Dicom Mosaic images can be saved as Nifti series directly without first converting. When a mosaic image series in loaded, the following option will be enabled on the image save dialog, activating the same mosaic definition dialog as shown above.

If multiple mosaic images are saved (e.g. an ASL time series or a perfusion series) then a single 4D Nifti file is generated by default. Multiple Nifti files can optionally be generated, as set under Options->Image Save on the main menu.

Note:

For older Siemens Mosaic formats, the image may not be automatically recognised as mosaic and the identification must be obtained from the Siemens Private DICOM tag: Sequence Parameter File Name. This is by default set to contain the string mosaic (i.e. the string must be present somewhere in the file name). This can be changed under Image Formats in Main Menu: Options->Settings->Image format:

Related topics:

Saving images in DICOM format