DCMTK

According to this newsgroup posting, the Modality LUT Transformation should not always be applied to the pixel data, i.e. even if it is present in the DICOM dataset:
https://groups.google.com/forum/?hl=de&fromgroups#!topic/comp.protocols.dicom/n5ybyj1Psno

Here's an excerpt from David Clunie answer:

By the way, in general, it can be difficult to decide whether or 
not to apply the conceptual Modality LUT step before windowing, 
even if it is specified by Rescale Slope/Intercept values rather 
than an actual LUT. For example, in MR images to which Philips 
has added the rescale values, these should not be applied before 
their window values; likewise in PET images, especially those 
with GML Units and rescale values to SUV (small decimal numbers), 
the window values are historically usually in stored pixel values 
rather than SUVs. Making the correct decision may require comparing 
the range of possible rescaled output values (across the domain of 
possible input stored pixel values) with the specific window values, 
to see if the latter "make sense".

Currently, the DicomImage class only ignores the Modality LUT Transformation for the following SOP Classes:

• UID_XRayAngiographicImageStorage
• UID_XRayRadiofluoroscopicImageStorage
• UID_RETIRED_XRayAngiographicBiPlaneImageStorage