Help! Problems creating clean 3D Models

[SJSato]

I need some help refining my 3D models! I have been using 3DSlicer to create .STL files from DICOMS. I have been focusing on isolating sections of the skull. The problem I have is as I adjust the threshold to isolate the bone, I either get a lot of extraneous bits and pieces of adjacent tissue or, the bone is isolated, but incomplete in areas. I Import the .STL into Blender and/or Meshmixer, but it seems like a crazy amount of work to clean up the model. Would I have better luck using OsiriX? There just isn't much in the way of documentation out there to get me started.

Thanks for any help!

[mplishka]

SJSato, the issue could be the DICOMS themselves.  The imaging parameters for the study might not have given the cleanest contrasts for segmenting and modelling.  Try some of the non-traditional settings when trying to isolate the bone.  Instead of using the bone setting, play with some of the other settings like muscle or vascular.  Sometimes they give better segmentation of bone.

 

Let us know how it goes!

 

Best of luck!

[SJSato]

I was thinking it maybe the DICOM files. I was probably a bit too ambitious in trying to cleanly segment too large of an area. I'll try to concentrate on a smaller region.

[Dr. Mike]

When you export to STL from Slicer or Osirix, it is common to get a lot of "islands" of mesh that were included in your segmentation. This is especially so it you use threshold to do your segmentation. If you load the STL file into Blender, select one vertex that is on the part of the bone you want to include. Then hit CTRL-L to select all vertices that are connected to that vertex. This should select your entire target structure BUT NOT the mesh islands you want to discard. Then, hit CTRL-I to invert your selection. Those islands are now selected. Delete them. 

 

That allows you to quickly get rid of all those extra mesh islands that are exported to your STL. 

 

For more detail about this, go to my tutorial page and view the video. Starting at 11:01, I describe this technique.

 

Hope this helps! I am really glad you are slogging through learning Slicer and Blender. Keep it up. They are tough to learn but once you get the hang of it they are very powerful. 

[mario.diniz@gmail.com]

I believe there are two important moments, the first is the threshold configuration in osirix when selection the tissue from tc, depending on how we set it, we have more work on the second moment which is in blender. Considering we´re talking about bones. Have you tried to extract soft tissues ? Like cartilage or veins ? How do you work with them ?

[kopachini]

I need some help refining my 3D models! I have been using 3DSlicer to create .STL files from DICOMS. I have been focusing on isolating sections of the skull. The problem I have is as I adjust the threshold to isolate the bone, I either get a lot of extraneous bits and pieces of adjacent tissue or, the bone is isolated, but incomplete in areas. I Import the .STL into Blender and/or Meshmixer, but it seems like a crazy amount of work to clean up the model. Would I have better luck using OsiriX? There just isn't much in the way of documentation out there to get me started.

Thanks for any help!

 

... or you could manualy segment that body part in 3d slicer, and than there is no big work needed in blender (this is excelent for small models, i know, but for larger maybe you should stick by earlier mentioned method of fine editing and postprocessing in blender)

[kopachini]

I believe there are two important moments, the first is the threshold configuration in osirix when selection the tissue from tc, depending on how we set it, we have more work on the second moment which is in blender. Considering we´re talking about bones. Have you tried to extract soft tissues ? Like cartilage or veins ? How do you work with them ?

 

i am using 3d slicer, and i adjust treshold at the limit where there is the least unwanted tissue marked, than i finish segmentation manualy.

 

 

but since i started reading this forum i have doubts if this method of manual segmentation is very time consuming, specially if very large models are planed, so i wanted to ask what is  @dr. mike's opinion on this.

should i stick to manual segmentation and then have very little postprocessing work in blender, or use other technique (fast segmentation in 3d slicer, and lot of postprocessing done in blender)??

[Dr. Mike]

I think it is best to invest the time to do a good segmentation in Slicer before exporting to STL. Once the file is in STL format and has hundreds of thousands of vertices, it can be really difficult to clean up.

 

One of the nice tools in slicer to make this easier is threshold paint. You can apply a threshold and choose a paintbrush and then "color" in your label map. The label map is only applied to the area your paint brush touches, and only if the threshold is met. This allows you to apply a threshold to a limited area where if you used whole-study thresholding you would include all kinds of objects you don't want to. You can find this tool in the Editor. See below.

 

[3dtech]

thanks for this valuable information.

[kopachini]

For my last segmentation of mandible, i used Level Tracing Eeffect tool but without threshold, and it was very easy and fast.

 

 

[Dr. Mike]

I'd like to mention that there is now a free service available on this website that automates the segmentation and creation of bone STL files, so you don't need to go through the steps with Slicer and Osirix. It's free for embodi3d members. Creating a bone file takes about 2-3 minutes to upload the CT scan in the correct file format (NRRD), then about another 10 minutes or so to process. You'll get a notification to your email address that your file is ready. Here is a lumbar spine model I made in about 5 minutes using the service. Also below is a link to a tutorial to get you up to speed quickly.