Hello,
I want to convert a deck of segmentations of multiple slices in a CT image made using ImageJ into usable input for pyRadiomics. For example, in the attached screenshot, you can see that I have 3 segmentations, one per slice in the CT (outlining a portion of a kidney tumor), and my goal is to save all three of them into a usable mask for pyradiomics, e.g., an nrrd file, so that the radiomic features are extracted only from the area inside each segmentation. Is this possible?
Thanks!
S
Should be real simple, if you use Fiji, which supports exporting NRRD.
Not really - the issue is that there are several slices here, each with their own segmentation, and when I save the image as nrrd, none of these segmentations show up on the nrrd file. I then tried to save the segmentations as an overlay (Image > Overlay > From ROI manager), but the overlay is done for a single ROI at a time. Am I missing something?
I am not all that knowledgeable with ImageJ/Fiji. I expect you should be able to export each of your ROI to its own imagestack first, and then save as NRRD. But that’s as much as I can help.
If you do not have extensive segmentation, it might be faster to redo the segmentations in Slicer and avoid all these issues.
Got it. Yeah, I think it would be easier to redo this in 3D slicer. Unfortunately, it’s a bit of work regardless of what I end up doing - a former colleague left me with 150 meticulously segmented dicoms using Fiji, and I was trying to salvage them. Thanks.
S
Then, ask in Fiji forums how you can turn those segment to separate binary image sequences. Once you do that, rest should be more straightforward.