Modifying Threshold to Clean up 3D images
If an image shows up when thresholding or making a 3D model is there a way to tell the program not to include this even though it falls into the threshold? How do you clean up your 3D image?
Hi Brian,
As you have noticed, thresholding is a global operation which selects pixels on all the slices. A good tool to isolate one structure from a mask is Region Growing. The Region Growing tool separates a stucture from a mask by growing out from a seed point and finding what is connected.
There is a good explanation of the tools parameters in the Help files, which you can find under Help -> General Help -> Mimics menus -> Segmentation -> Region Growing.
Additionally, many of the tutorials within Mimics show how to use the Region Growing tool. You can find the tutorials under Help -> General Help -> Mimics Tutorial. Tutorials such as Mimi and Hip both have steps that include using the Region Growing tool.
Using the Region Growing tool is simple and straight forward. Once you open this tool and set the parameters to fit your needs, all you need to do is click on the object that you want to separte out from the existing mask. The Region Growing tool will use the point that you clicked on as the seed point and check if the adjacent pixels are connected in the mask. Once the operation finds a pixel that is not connected, it will stop growing out.
If the region growing as described by Eric still selects too much (when the voxels are connected), you can use the crop mask function to delete the mask outside a bounding box.
After that you should resort to editing options; Edit mask in 3D can be very helpful in the sense that you get a 3D preview of your mask and your edits.
I am trying to seperate muscles with quite similar thresholds and calculate 3D images of all the muscles in leg. As they are quite similar region growing is not ideal. Can you suggest the best way to seperate out the different muscles?
As muscles are close together and within the same threshold, it might be better to do a contour based segmentation; try using the 3D LiveWire or clean up the mask with the editing tools Floodfill or LiveWire (available in the drop-down in the editing toolbar). Asssuming you can visually distinguish the different muscles?!
You might try to play a bit with morphological operators. They can do wonders...
Good luck,
Ulli