general > RE: Welcome to General forum for QuickNII
Apr 3, 2019  06:04 AM | Gergely Csucs
RE: Welcome to General forum for QuickNII
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.

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TitleAuthorDate
Gergely Csucs Dec 14, 2018
Harry Carey Apr 2, 2019
RE: Welcome to General forum for QuickNII
Gergely Csucs Apr 3, 2019
Harry Carey Sep 11, 2019
Harry Carey Aug 27, 2019
Gergely Csucs May 29, 2019