By: M.Zubair on June 30, 2022, 3:44 a.m.
Hi Everyone,
Greetings!
I am working on a database published on TCIA in DICOM format. I am able to view all allother slices (DICOM file) for PET and CT in 3D slicer but the SEG directory for each patient just has one DICOM file. I am unable to view that. I tried 3D slier, python scripts but not work. Any face a similar issue or I am on the wrong side.
Lokking forward to hear from you.
By: thomas.kuestner on June 30, 2022, 8:55 a.m.
Hi,
did you try to load the SEG DICOM file with ITK (e.g. simpleitk via python)? This would allow you to convert it to any file format of your choice. In case you are referring to the TCIA database related to this challenge: We have verified correct loading of SEG DICOMs in various viewers and APIs (3D Slicer, MITK, Python, Matlab) and would need more information from you if you are having trouble here.
Kind regards Thomas
By: sergios.gatidis on June 30, 2022, 9:02 a.m.
Thanks for you question! The DICOM segmentation object format is a little peculiar. A good tool for looking at images and segmentations is MITK (https://www.mitk.org/wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK)) Slicer should also be possible to open this format but requires extensions (DCMQI) The DICOM segmentation objects can directly be read using pydicom. We recommend also looking at our provided conversion scripts* (https://github.com/lab-midas/TCIA_processing).
