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Hi, I am currently trying to export huge numbers of png slice images from QuickNII, up to fifty thousand at a time. 
One problem I am having is it seems that having to export .flat files, which I don't need for my purpose, slows down the export process immensely as they are much larger than the corresponding png files. Is there a way I can disable the exporting of the .flat files and only export pngs?
Any help would be greatly appreciated

There will be some example code released about working with QuickNII output, but I guess you may need this help sooner than in a couple months. http://www.nesys.uio.no/QSlicer/QSlicer.... is a package containing the necessary files for exporting those .png-s for both WHS and ABA.
Some assumptions/requirements:
- Windows (but it is not an absolute requirement, see last line of this message)
- fully propagated QucikNII XML (the "Export Propagation" button has to be used - btw, that button does not append .xml extension automatically, so it has to be typed manually)

Then copy the XML file into some empty folder, launch the corresponding .bat file, pick the XML in the dialog, and see what happens. Usually it works.
This one still exports binary segmentation, but in compressed format. If you happen to plan using Matlab, here is the code for reading those .bin files:

    % Read "filename.bin" segmentation file in Matlab
    stream = java.io.ObjectInputStream(java.util.zip.InflaterInputStream(java.io.FileInputStream("filename.bin")));
    array = stream.readObject;
    stream.close;

where "array" is going to be a 2D array containing segmentation identifiers (also, the gist of it is Java - Matlab has built-in Java).
If you absolutely do not want the .bin files either, the "binobj=true" parameters at the end of ABAv3\doABAv3.bat and WHSv2\doWHSv2.bat can be removed. But the binary segmentation really has its use if you ever plan to do any kind of computational processing of the images: the colours are not unique, there are repeats even in the WHS Rat. The identifiers are unique.

If you happen to use Mac, Linux, the tool can still be run from the command line, it just needs a Java runtime. Refer to the doXY.bat files mentioned above for command-line parameters.

Source code for a NIfTI slicer utility (NIISlicer) has been released on GitHub: https://github.com/Tevemadar/QuickNII-extras/tree/master/Java

Thank you so much! apologies for the late reply, this was hugely helpful :)

This tool was hugely helpful however now it seems the link 404's, is there anyway you could re-upload QSlicer? 
The help is greatly appreciated.