Surface representation of segmentation is too much smoothed


I have been doing segmentation for EAT and Ventricles. I use manual segmentation by hand. Whenever I look at the 3D Model generated by 3D Slicer, I see that there are gaps between slices even if I segmented every slice… I need to generate 3D Volumes based on my segmentation.

I also figured that whenever I drag my .nrrd and .seg.nrrd files into 3D Slicer, my segmentation seems less than what I make. If the segmentation is thin, 3d Slicer assumes that there is nothing there,I am guessing. Is there anything I can do about it? I would appreciate if any of you help me.

You can find the pictures at the atachment,

Your help is highly appreciated in this matter.


This is a common issue when the input volume is highly anisotropic. I would recommend to always use Crop volume module to resample the input volume to an isotropic voxel size before starting segmentation.

You can of course also turn off smoothing during model generation (in Segment editor module, click the small arrow on the Show 3D button and set surface smoothing to 0), but then the reconstructed surface would have staircase artifacts.