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In order to resolve the vendor-specific data format inconsistency, improve efficiency, and allow for generalized parameter headers, Siemens decided to transition to using Enhanced DICOMs to store functional, DW, and ASL images. The Enhanced DICOM format is new to Siemens, but was first proposed in 2005 by the DICOM Standards Committee. Philips began supporting the format as an optional feature in 2008. At the time of writing it is still unclear if GE supports Enhanced DICOMs or not.(I'll update this post when I have firm information on that point.) The Enhanced DICOM format saves slices in a 4D matrix. The 4th dimension is not generally used for functional, DW or ASL imaging, but is available for repeated measurements of the same type. Instead, the format will usually have this dimensionality:
nRE x nPE x 1 x nS× nPE × 1 × nS
Where, nRE is the number of points int he read (or frequency) encode direction, nPE is the number of points in the phase encode direction, and nS is the number of slices. This format resolves the square number of slices issue from the mosaic format while keeping its single-header efficiency. Also, the Enhanced DICOM format allows for slice-by-slice acquisition headers, which is a general solution to parameter storage.
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At the time of writing, Chris Rorden's dcm2niix is the only conversion tool we are confident will work. We worked with Chris to independently validate all the parameters in a wide variety of use cases scenarios. These validations pass his QA tests and match our measured data. However, these changes only exist in v1.0.20181022 and later, so be sure you're up to date! Usually, the preferred method to get dcm2niix is as part of the MRIcroGL package. But, until the current stable release of MRIcroGL is updated to include the updates to dcm2niix, you will have to download and compile it from the GitHub link at the beginning of this paragraph.
Admonition Against the Use of Mosaics From NX Scanners (Like the Vida)
At the time of writing, there is no way to disable the creation of mosaic DICOMs for functional, DW, and ASL scans on the Siemens Vida scanner. But, the mosaics don't have much information in their headers, and almost none of what is needed to process data using mainstream pipelines. So, it is imperative that you not attempt to use them for scientific analysis. Note that this does NOT apply to the Siemens Skyra scanner. Mosaic DICOMs are the primary and MUCH preferred format to export data for that generation and virtually every other generation of operational Siemens MR scanner. Mosaic DICOMs are only problematic when they come from NX scanners, and at the time of writing, the Vida is the NX-line scanner.