Converting Siemens MOSAIC

March 21, 2010

(This article was first published on Rigorous Analytics, and kindly contributed to R-bloggers)

Siemens multi-slice EPI data may be collected as a “mosiac” image; i.e., all slices acquired in a single TR (repitition time) of a functional MRI run are stored in a single DICOM file.  The images are stored in an MxN array of images.  The function create3D() will try to guess the number of images embedded within the single DICOM file using the AcquisitionMatrix field.  If this doesn’t work, one may enter the (M,N) doublet explicitly. 

The first image is taken from the raw DICOM file, in mosaic format, and displayed with the default margins [(5,4,4,2)+0.1].

The second image is displayed after re-organizing the original DICOM file into a 3D array and then converting it to NIfTI format. Additional information, using the valid NIfTI header fields descrip and aux_file, have been defined for these data.

Remember, all other Siemens DICOM data are stored as a seperate file for each image (as is the case with the other major MR scanner manufacturers).

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