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 …

Hi thank you for the reply! So from my understanding we either need to acquire isovoxel scans or try to use NiftyMIC to see if it could work is that correct? is it possible to segment individual planes e.g if I segmented using the Coronal plane scan then segmented the Axial plane scan (both high qu…

As it is described in the post I linked, you can resample any of the input volumes to be isotropic using the Crop Volume module. Then the segmentation you create for it will be isotropic, too. You can represent structures with finer details in this segmentation than in any of the input 3D volumes. T…

Hi, I’m not quite proficient with 3Dslicer. I’ve tried playing around with the crop volume module but with no luck on how to do what you mentioned before. Is there a guide / tutorial anywhere explaining how to achieve this using the crop volume function? I also looked at NiftyMIC and the main prob…

[Cropping a Volume [3D Slicer Workflow]]

Hi guys, Thanks for the help! I managed to acquire 3D scans (I believe isovoxel?) however when I try to segment its very pixely / block like. Any ideas what cause be causing this? Im just using the segment editor function with the sphere brush. I just need the pixels slightly smaller to be able to s…

For context these are medial recti muscles.

[image] teakpAUM: PixelSpacing : 0.9375, 0.9375 Slice thickness: 0.89999997615814 Pixel spacing is not bad, but we don’t know the distance between slices. If that is around 1mm, too, then your image should not be very “blocky”. You can find all 3 components of the image spacing in Volumes mo…

Hi Andras, This is the spacing: [image] Seems like oversampling works to fix it. Although I dont know if selecting that and isotropic spacing on the ‘segmentation geometry’ will skew my volume measurements for my project?

Resampling will not invisibly skew volume measurements. Volume is measured from the segmentation as displayed: what you see is what gets measured. If your segmentation accurately follows the original image (contours are aligned with visible boundaries, no details are lost due to insufficient resolut…

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

Support

lassoan (Andras Lasso) January 12, 2026, 5:40pm 2

This is a very common limitation of clinical images that are acquired for slice-by-slice reading by humans, and not for 3D processing. You can find how to deal with such images for example here:

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

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