![]() ![]() In fact, for many (most?) things I use pydicom, but for any true 3D type work, SITK is the easier toolkit to use. dicomanon (filein,fileout,'keep',fields) modifies all of the confidential data except for those listed in fields. Image data and other attributes are unmodified. This isn't something bad about pydicom, but more a question of right tool for the job. dicomanon (filein,fileout) removes confidential medical information from the DICOM file filein and creates a new file fileout with the modified values. It only gives you the raw pixel arrays (for images). Pydicom, in contrast, doesn't itself try to use any of that information at all. So - in your case - if you use SITK to open your studies, then you should be able to overlay them correctly "out of the box", because SITK will do all the work to parse the Image Plane Module tags and locate the data in patient coordinates - just like you get with 3DSlicer. The simple ITK library fully understands and uses the full 3D Image Plane tags to identify and locate any images in patient coordinates by default - irrespective of such things as the specific pixel spacing, slice thickness etc etc. This uses a bunch of attributes in the dicom files in the Image Plane Module set of tags. For what you want it sounds like you should use Simple ITK (or equivalent - my experience is with sitk) to do the dicom handling, not pydicom.ĭicom has built in a complete system for 3D point and location specifications for all the pixel data in patient coordinates. ![]()
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