Issues with segmentation pixelation and resolution when using separate Axial/Coronal DICOMs.

teakpAUM
Mon, 12 Jan 2026 16:36:52 +0000
Support

I’m working on a project to segment structures within the orbit. I’m using fat suppressed T1 weighted images from a database. The MRI DICOM files are downloaded individually e.g. one will be coronal one will be axial. But they’ll both be from the same patient. So they’re the same scan but different protocols. I’m importing the axial and coronal scan from the same patient into one file. Then I’m opening the folder on 3D slicer which has both the scans in. I ran into an issue that when viewing the scans e.g. I’m looking at the coronal scan 3D slicer then renders the other planes in awful quality so I cant segment using them.

When I try to segment in only one of the files e.g. the coronal file and then look at the axial file the segmentations roughly overlap but become extremely pixelated and blocky. When I try to change the segmentation on that scan (the axial) it only does large wide pixels. I would’ve expected if I segmented on the coronal scan for the axial to match roughly and then I can fill in the blanks using that axial scan. But the way its so pixelated I cant work on it at all.

Based on the practice scans, all three planes were clear and visible such that I could segment freely - my segmentation on one plane would show up correctly on the other planes and this would generate a correct 3d image in the fourth window. Is there any way to achieve this with the scans I’m downloading? Maybe so that the separated clear planes in each scan could be merged so I can view and segment on them at the same time.

11 posts - 3 participants