Thank you for the image! Do you feel comfortable executing Python scripts? In that case I asked ChatGPT to create a script to convert DICOM images like yours to a single channel grayscale image which you then can easily use in MITK with the Statistics plugin. I attach the script. As prerequisite, you need to install SimpleITK and numpy with pip: "pip install SimpleITK numpy". Then, execute the script like:
python convert_dicom_grayscale.py P1FA4OOE which will create an image file at the same location named P1FA4OOE_grayscale.nrrd. Best, Stefan ________________________________________ Von: Delvaux Bernard <delvauxbern...@yahoo.fr> Gesendet: Mittwoch, 12. Februar 2025 12:59 An: mitk-users@lists.sourceforge.net; Dinkelacker, Stefan Betreff: Re: AW: AW: [Extern] - [mitk-users] Retrieve segmented surfaces Thank you Stefan for your kind answer. As far as I know it is a raw DICOM file extracted from US machine Logic E10s (GE Healthcare). The file is totally anonymized and I will send you a link to download it. Regards, Bernard Le mardi 11 février 2025 à 23:41:20 UTC+1, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de> a écrit : I see, I will extend the ticket to not only handle unsupported pixel types more gracefully but to maybe also still show statistics that do not depend on the pixel type like volume and number of pixels of labels. I am afraid none of this will resolve your issue in the short term since code changes are required. The empty pixel type is interesting, can you tell us more about the image or in case it is anonymized give us a sample so we can look up what is going on? Best, Stefan ________________________________________ Von: Delvaux Bernard <delvauxbern...@yahoo.fr<mailto:delvauxbern...@yahoo.fr>> Gesendet: Dienstag, 11. Februar 2025 19:43 An: mitk-users@lists.sourceforge.net; Dinkelacker, Stefan Betreff: Re: AW: [Extern] - [mitk-users] Retrieve segmented surfaces Hi again Stefan, and thank you again for your help. I want to measure the surface of a label indeed. And more precisely, calculate metrics (like DSC, IoU, precision and recall) of 2 labels in a single slice (for now; we consider expanding to 3d meassurements later). I already used the method you recommended with Horos: I measured by hand the 2 surfaces and their overlap by hand and I was able to calculate everything I wanted. So it is possible but time consuming, and also less precise than automated calculations. This is why I'd like to use a software with segmentation capabilities for that purpose. Thanks Bernard Le mardi 11 février 2025 à 10:56:54 UTC+1, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> a écrit : Sorry, sent again to include the MITK Users list. ________________________________________ Von: Dinkelacker, Stefan Gesendet: Dienstag, 11. Februar 2025 10:54:43 An: Delvaux Bernard Betreff: AW: [Extern] - [mitk-users] Retrieve segmented surfaces Hi again, by "surface", do you mean a segmentation label, resp. masked pixels and only in a single slice? Or all the pixels of a segmentation label (volume)? Or, surface in the sense of MITK, which would be a 3-d polygon mesh? The volume of segmentation labels is shown in the statistics plugin, but I already read that you have trouble with unsupported pixel types, right? If you are really just interested in the 2-d area of something in an image, and you just created segmentations for this purpose, an alternative would be the Measurement plugin, where you can draw a (smoothed) polygon for example to see the circumference and area in mm². Best, Stefan ________________________________________ Von: Delvaux Bernard via mitk-users <mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net><mailto:mitk-users@lists.sourceforge.net>> Gesendet: Montag, 10. Februar 2025 07:54 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net><mailto:mitk-users@lists.sourceforge.net> Betreff: [Extern] - [mitk-users] Retrieve segmented surfaces Hello, I'd like to know please how to retrieve the area of segmented surfaces, including intersection and union surfaces calculated in Boolean operations. I've been searching for this without succes and I'm new ti MITK Workbench. Thanks, Bernard
convert_dicom_grayscale.py
Description: convert_dicom_grayscale.py
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