Surface Area Calculation

[David Russell]

Does anyone know an easy way to get ITK-SNAP to output the surface area in mm2 of a manually segmented volume?? 

BW

Dave

[Paul Yushkevich]

This would not be exact, but a reasonable approximation. Assuming your structure of interest has label 4, do the following in c3d:

c3d my_seg.nii.gz -thresh 4 4 1 0 -voxel-sum -dilate 0 1x1x1 -voxel-sum

This will print the volume of the structure of interest before and after erosion by 1 voxel. Essentially, erosion takes the outer layer of voxels off, which corresponds to surface area. If your voxels are anisotropic, this won't be correct, and you would need to first resample your image (using -int 0 to get nearest neighbor interpolation and -resample-mm) to isotropic resolution.

The other approach is to export your segmentation as a mesh, and look for mesh visualization tools that can report surface area. I am sure some do, but don't know off the top of my head.

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[David Russell]

Thanks I will give it a bash. Interestingly, I tried to use meshmixer. It can import stl meshs and calculate their surface area and volume. When I tried it with ano stl mesh I had extracted from itk it loaded up fine and calculated a Surface area and volume. The volume however was considerably different from ITK snaps calculation. Is there anywhere with a collection of unit volume meshs/segmentation phantoms for testing. Thanks, again for the help.

[Paul Yushkevich]

David

The difference may be due to the fact that by default ITK-SNAP applies some smoothing to the segmentations before creating meshes. You can control this behavior under Preferences, 3D Rendering. I would hope that after that, the volumes from the two tools would be consistent.

Paul

On Mon, Oct 5, 2015 at 8:15 AM, David Russell <rgbrg...@googlemail.com> wrote:

Thanks I will give it a bash. Interestingly, I tried to use meshmixer. It can import stl meshs and calculate their surface area and volume. When I tried it with ano stl mesh I had extracted from itk it loaded up fine and calculated a Surface area and volume. The volume however was considerably different from ITK snaps calculation. Is there anywhere with a collection of unit  volume meshs/segmentation phantoms for testing. Thanks, again for the help.

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[Bin Paul]

Hi Paul,

I am evaluating picture of dimple found on the female cheek. I need your help what is the best way to evaluate the dimple size (length, depth or width) using ImageJ or any other tools. If we used pixel, I am wondering how to calculate, how much pixel is equal to one centimeter or cubic centimeter? in other words, how can we convert pixel to centimeter?

Thank you for your help in advance.

Bin

[Bin Paul]