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I have to segment a few things in a dataset I have (.nrrd-file) by drawing a rectangle around the area of interest and saving the segments (also as .nrrd-files).

I tried everything in the Segmentation-Tool that comes with MITK but I cannot seem to find a way to draw rectangles. I also tried to do some key combos (like holding shift, ctrl or alt) while drawing but in vain. I know I can use the Measurement-Tool to select rectangles and save them (as .pf-files), but using that I'd have to write a some code to convert those selected rectangles into rectangle segmentations later on.

Does anyone know whether there's a possibility (that I didnt find yet) to draw rectangles in the Segmentation tool, or some other way so there's no need to write a workaround?

DrSkyer
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1 Answers1

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You can use the Image Cropper plugin in MITK 2016.11 for rectangular image masking and cropping (scissors icon).

Open the plugin, select your image in the Data Manager and click on the New button in the plugin to create a bounding object. You can modify the rectangular bounding shape in the render windows by dragging its red handles. You can move the whole shape by hovering over the bounding shape (it will turn green), click, and than drag.

Click on the Mask button if you want to get an image with the same dimensions in which all pixels outside the bounding shape are set to a user defined value (see the Advanced settings in the plugin). Click on the Crop button otherwise.

Note that you can always press F1 in any active MITK plugin to open a help page with detailed instructions.

S. Dinkelacker
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