Dr. Mike

Great comment Flaviu. Thanks for sharing your thoughts. Do you have any direct drive printers you recommend?

What printers do you think are better for clinical in-house printing?

That is a large file! I would recommend cropping the NRRD file to only the volume you need. Much of the size of an NRRD can be the air that is around the subject. You can use the Crop Volume tool in Slicer. This tutorial shows how.

Arish, This is a pretty old thread and things have changed in the years since it was started. What exactly are you doing. There are many more software options now. If I knew what you are trying to do I can point you in the right direction. Dr. Mike

Democratiz3D uses a threshold segmentation method. You can adjust the threshold value (in Hounsfield units) to control what structures you want included or excluded, based on their density. This works best for bones. Since you want to segment only the collecting system, you can give contrast and do a delayed phase CT to show the contrast is the collecting system, but you will still have the issue of the bones being included too. The best way to deal with this is to create a subvolume of your CT scan. That is only include the volume that contains your collecting system and exclude the bones. This tutorial shows you how to use 3D Slicer to create a NRRD file that has a subvolume with the Crop Volume tool. Once you have cropped your volume, upload the subvolume NRRD file to democratiz3D and it will spit out your collecting system. If a few small bone chunks are still present, you can manually delete from from your STL file using Meshmixer, Blender, or some other mesh editing software program. Hope this helps.

I agree with kopachini. A good arterial phase can be automatically segmented using the correct threshold level. The default of 150 is probably OK, but you can adjust this to meet the specific parameters if your scan. Check to see what the hounsfield density is within a major vessel, such as the aorta, on the arterial phase of the scan. Venous phase is more difficult because by the time the contrast is in the veins there is also usually organ enhancement and the organs will be included in the threshold segmentation. If you have a scan with the right kind of contrast enhancement however, it will work. If the scan isn't perfect, then you may have to fall back on manual segmentation using software like 3D slicer. Hope this helps.

With a sharp or bone reconstruction kernel you are still going to have unnatural edge enhancement. These algorithms are designed to provide maximum conspicuity of fractures, not accuracy of the bony surface. The soft tissue algorithm will provide a truer approximation of the real bone surface.

Andreas, thanks for posting this update in this thread and for your continuing work with 3D Slicer. Please continue to update us in this forum regarding new features to Slicer. Dr. Mike

How much bigger are we talking about? Are you off by 10% or more like 100%

sam17franklin, thanks for the post. Which conference did you attend? The reason I ask is that I attend and often present at most of them, so I am curious. RNSA? Mayo 3D Printing? Raw data from a CT scan is useless from a 3D printing standpoint. It is the raw data that is acquired from the x ray tube spinning around the patient in a helix. FROM the raw data axial, sagittal, and coronal image series can be generated by computing the attenuations at given rotation angles and converting that into a matrix that can represent a "slice" in the stack of images. From the raw data you can generate 5mm slices, or 2.5 mm slices, or 1.25 mm slices, or 0.75 mm slices, although with diminishing image quality the thinner you go. Raw data is used to generate the standard slices from a scan, and then it is typically deleted from the scanner to save storage space since it consumes a lot of it. I think what the radiologist meant was that if you have access to the raw data, you can reconstruct a scan with very thin slice intervals (1.25 mm of less) for 3D printing that may not have been generated as the default slice thickness for that type of study. I agree with the radiologist's advice on soft tissue reconstruction. Soft tissue is a kind of "soft kernel" reconstruction as described in my tutorial about choosing the right scan for 3D printing. Bone reconstructions are grainy as they are a type of "hard kernel" or "sharp kernel". They are designed to make it easy to see fractures, and thus have a lot of edge enhancement applied to make edges appear unnaturally noticeable. Look at the picture at the bottom left. Notice that right outside the bone is unusually dark? That darkness isn't really there. It is a artifact of the algorithm and is designed to make the bone-tissue interface have higher contrast. This makes it easier to see fractures but isn't good for 3D printing because the pixels are noisier, i.e. they look speckled like a photograph in low light. Any bright pixels confuse the software because it thinks there are thousands of bright, pixels-sized speck of bone everywhere, but really it is just noise. Each bright pixel can therefore be converted into a speck of bone in your model. Bone and lung reconstruction algorithms have this type of edge enhancement. Soft tissue reconstruction algorithms are best for 3D printing because they don't have the speckling and thus don't generate a "sea of sand" when converting to a model. Hope this helps.

embodi3D doesn't host DICOMs because they aren't anonymized by default and there is a risk of inadvertent sharing of patient information. The NRRD format is anonymized and thus safe to share online. If you are using 3D slicer and want to manually extract the bones, you can do so easily with NRRD, which kopachini has already sent you a link to the extensive femur scan library. 3D Slicer can process both DICOM and NRRD, with the only difference being time to load the scan (DICOM is slower). Of course, if you DON'T want to manually extract the bones you can send the NRRD file to the democratiz3D service on this site, and it will generate a 3D printable model for you in about 10 minutes. Just another option for you to consider. Hope this helps. Dr. Mike

I'd like to elaborate on this topic a bit, as I recently had another member inquire about this issue. The member was creating a model from a CT scan of the clavicles. As you can see, there are holes in the medial (midline) ends of both clavicles. What is causing this? Is it a problem with democratiz3D? How can it be fixed? The issue lies with the patient's anatomy and the quality of the original CT scan. In the human body there are areas where bones are naturally very thin. Sometimes, the bone surface (cortex) can be paper thin. Also, some patients who have conditions like osteoporosis may have very little calcium in their bones. Issues like this make it very hard for the CT scanner to detect the bone wall, as you can see from the image below which shows the area on the left clavicle that has a hole in the final model (red arrow). The problem isn't with democratiz3D, but with the quality of the CT scan or with the patient having thin bones (how dare they!). democratiz3D is actually creating the model exactly as it appears on the CT, its just that the CT has holes we don't want! So, what can be done? If you encounter this problem you have two options. 1) Manually fix the holes in the model with a mesh editor like Meshmixer, or 2) decrease the threshold value in democratiz3D and re-process the scan. Decreasing the threshold tells the system to capture more voxels in your model, potentially capturing more thin or osteoporotic bone. But, be careful. If you reduce the threshold too much (less than 100), you run the risk of starting to capture muscle, organs, and vessels in your bone model. If you are not sure what threshold to use, you can experiment by running your scan through democratiz3D using different thresholds. To save time, I suggest you do this on low or medium quality setting. When you find a threshold that works, you can generate your final model using a higher (and more time consuming) quality setting, like High or Ultra. If you are familiar with mesh editing software, that is probably the fastest way to correct this problem. Just delete the edge of the hole, fill it in with a new face, and run a quick smooth operation on the area. It's a 1 minute fix if you know the keyboard shortcuts. I hope this tip helps. Dr. Mike