Lumen of vessel in 3D Slicer

[jscales1]

How does one use 3D slicer in order to generate the lumen of the vessel?  Selecting the artery on a CTA basically gives you the lumen but I would like to know how to "wrap" (as they call it in Mimics) with 3D slicer or Blender.  Mimics seems exactly like 3D slicer except for a few more bells and whistles. Really aiming to try and get a model like Dr. Mike's splenic artery aneurysm model except with an infrarenal fusiform AAA. Just trying to further hone my 3d printing skills after the excellent work and guides that have been done on this forum. Thanks

[Dr. Mike]

Export the lumen as STL and then import into blender. Create a sphere with lots of polys and use the shrinkwrap modifier to wrap it around your lumen. This is your inner surface. If you need to, you can use the remesh modifier until you get the right poly count. Reverse the normals on the inner surface so they are pointing inward. This method of using shrinkwrap and remesh was described in my prior tutorial on correcting mesh errors in bone STL files, but you can use the same method for vessels. The idea is the same -- generate a clean surface that closely approximates your target surface. Although for hollow vessels you are creating two surface (inner and outer)

 

Repeat the sphere and shrinkwrap and set offset to 2 or whatever you want your thickness to be. This is your outer surface. Leave the normals pointing outward. Join the two and you should now have a hollow structure with an outer surface and an inner surface. Cut holes in your object to open it up at various points as desired. If you are making a AAA, then you'll probably want to cut above the renal arteries, in the distal aorta or common iliacs, and you'll want to trim the bilateral renals. 

 

If you would like to to help you with this specific file, please message me. I do this a lot and I think it will be pretty easy for me to get you on the right path. What are you doing this for?

 

If there is interest in this forum for me to do a formal tutorial on how to do this, sound off here. If there is enough interest I'll create one.

 

Best,

 

Dr. Mike

[jscales1]

Dr. Mike,

   Thanks for the video hotlink. I wouldn't have even tried looking through that video for the shrinkwrap and remesh tool. Very good to know. 

 

I just received a 3d printer, Lulzbot Mini, and I am trying to create 3d prints to show to my patients during consultation. One area I feel like it would be great for is exophytic renal lesions prior to cryoablation. I have made a renal model, albeit kind of pathetically, with both Slicer and Blender. The AAA is just to get my feet wet with CTA images and producing a model with a lumen such as the splenic artery model you created. 

 

Love the forum and really think this is the next big area for IR to grow into and become leaders. 3D printing is truly amazing. Keep up the good work and thanks for the link to the video.

 

J. Scales

[Dr. Mike]

If you are going to be at RSNA this November or SIR in April, I am giving several 3D printing talks and hands-on sessions. I'd love to talk to you in person. 

 

If you have any questions or need help, ask on the forums or message me. Happy to help in any way I can.

[jscales1]

Unfortunately I will not be at RSNA this month. I may be in attendance at SIR, waiting for my schedule to be finalized prior to making travel arrangments. This months Radiographics has two articles, Medical 3D Printing for the Radiologist and Three Dimensional Modeling, discussing 3D printing and the radiologists role in this emerging field. Pretty neat stuff to see it finally come to a major journal. Also used Blender to Meshlab to smooth out my kidney model with an exophytic RCC with great results.

 

Dr. Mike any recommendations for Blender tutorials? I have been watching some youtube videos and they seem helpful.

 

J. Scales 

[kopachini]

Hi Dr. Mike,

 

I am new to 3D modeling and i find your tutorials and forum to be very helpfull and educating

 

 

I am reading this thread about adding lumen to the vessels and i see you have different aproach to this problem. Looking at your models of vessels I thought that modeling a 3D vessel should be easy, but i was wrong :/

 

I made 3D model of AAA, AIC aneurism and AFS aneurism, and I used Solidify Modifier in Blender to add thickness of 2mm to the model, so I am wondering is it a good aproach, more easier or i should stick to your idea??

Unfortunately I still don't have 3D model made so i can't inspect it more closely.

 

 

V. Kopacin 

[Dr. Mike]

The problem with solidify modifier is that it creates overlapping surfaces. Imagine a tree that has two branches -- one going right and one left. If you offset both branches evenly their surfaces with intersect near the base. It is a huge pain to correct this. I am working on a method to generate vascular shells quickly and accurately, but it is in development. If you get really stuck and need a hand, message me and maybe I can generate the hollow model for you from a solid lumen STL file.

 

Dr. Mike

[vlad]

I've been playing with "solidify" and "hollow" options in Meshmixer to create a vascular lumen with mixed results (hollow works much more predictably than solidify). Am I to understand that Blender or perhaps Mimics are the only other software that do this? Does Meshlab or any other (free) software have a feature to control vascular (or airway, duct, etc) wall thickness? It sounds from this discussion like Blender is the freeware package to learn in order to do this correctly for now, but I'm trying to specialize in non-Blender software as we have a Blender specialist where I work. So far I've seen alternatives and work-arounds for anything Blender can do for 3D modeling, even if it's in different packages or even combinations of other software. But wall thickness control is a big deal for vascular models. Is it time to bite that bullet and dive into Blender?

[kopachini]

Hi, sorry for not replyig earlier, I was on vacation for a few days.

 

First, thx for your  offer, dr. Mike. I want to learn how to do it so in the future this won't make problems to me , but if i get stuck I will contact you.

 

Second, let's say that I managed to overcome that "solidify" problem... Now, guys that I have contacted for 3D printing service told me that for an aorta with it's branches model will have to use a supportive materials, and they have huge problems with "hanging" parts (over 45*). Plus, I wonder would it be as smooth as yours models? What materials and type of printing did you use?

 

And, something i didn't consider as a problem is that aneurism of right AIC is so big and proximal to bifurcation, when i put 2mm vessel thickness, it touches left AIC, and that also makes big problem for printing guys.

 

How to overcome this problems??

PS. i am waiting for a reply of printing guys on my given ideas, too.

 

 

 

V. Kopacin

[Dr. Mike]

Can you post a screenshot of what your vessel looks like? I'm not sure what your printer people mean because overhangs are usually easily overcome with appropriate support.

 

Mike

[kopachini]

damn, how can i post a screenshot??

 

in the meantime, i contacted other guys, and thay said it is challenging but possible.

started some test prints and it looked good. 

[Dr. Mike]

Upload the picture to the Gallery, then include it by clicking the My Media button to select the picture and embed it in your response. 

 

Hope this helps.

 

Mike

[kopachini]

[Dr. Mike]

Well that looks like it should be printable. I recently printed a bunch of arterial models for the Society of Interventional Radiology meeting last month. In one case I made a complete arterial system from the diaphragm to the ankle. As you can see, they were much more complex than your model. I used stereolithography on a Form2 printer. Yes, you need supports, but that shouldn't be a big deal and your printing people should know how to do that. Let me know if I can help you any further.

 

[kopachini]

Yesterday got my model of aneurisms. It is made od PLA plastic ( it is cheaper ). Didn't want to wait another week for transparent filament.

Maybe my nex project will be made of transparent ABS and will look a lot cooler like your models dr. Mike

[kopachini]

@dr.Mike, regarding to your vascular models, I was wondering, what type of 3d printer do you use for printign wascular models, is it SLA/SLS type? And what are the prices of 3d models printed in SLA/SLS printers in USA (per gram or per time of printing)?

 

Last week i got offer for this same model as above for printing with SLS printer and price was exactly 1000€, wich is, unfortunately, too much for me.

[Dr. Mike]

I mostly use a Form 2 SLA printer by Formlabs. The cost of the resin is about $150 USD for 1 liter. I actually did a review on the Form 2 printer a few months back. The cost for a print is usually on the order of $10 to 15 in resin costs, plus time. The main problem with the Form 2 is the limited build volume. Larger SLA printers are available but are exponentially more expensive.

 

If you are trying to do a single print, have to tried looking into 3D Hubs? There might be someone with a Form 2 printer near you that can help.

[froth]

how you fill the gap between the inner and outer surface after shrinwraping? they re not connected even though joining them into one object?

 

the problem is also with outer surface which seems to be less accurate then inner surface. I guess its because of the shrink-wrap offset which must be about 2mm to build the thickness of the vessel wall.

the problem is particularly seen in more complex irregular meshes.

Dr. Mike do you have a solution for it?

[kopachini]

Outer surface dosen't have to be so accurate, inner surface is the real lumen of the vessel.

 

Dr. Mike, since I don't use shrinkwap modifier I have a question. When you use it, does it overcome the problem of the overlapping of the outer surface when the vessels are really close to each other (I presume that this kind of anatomy is still problem).

 

Few days ago I tried different approach: open the model in the Meshmixer, select all and go to edit menu and choose offset (set it on 3 mm or whatever thickness you want), and then delete inner surface. You can corect model near bases if there is overlapping with sculpt modes. Make new model (od outer surface) than import it in Blender and again use solidify modifier and offset 3 mm inside. I think that should solve the problem of overlapping near the bases. But still there is that one of anatomy that i mentioned earlier.

[froth]

I closed the cut edges of outer and inner surface with extrude and scale but still is a hidden space between these to layers. I think this is the reason why i Have problem with proper use of boolean modifier to later add the supports to the model.

So what are yours method of filling these two surface?

[kopachini]

3 hours ago, froth said:

I closed the cut edges of outer and inner surface with extrude and scale but still is a hidden space between these to layers. I think this is the reason why i Have problem with proper use of boolean modifier to later add the supports to the model.

So what are yours method of filling these two surface?

I don't fill those surfaces, I use solidify modifier so there is no need to merge two edges after offset.

And, maybe it is confusing, but even when you do solidify or whatever, you will still have "hidden space" between two surfaces (inner/outer shell...). When printing, 3D printer doesn't recognise that space as empty yet it is prints it as solid, full...

[froth]

I am not sure if dealing with solidify modifier is safe procedure. I tried a lot, every time something was wrong. I mean complex geometries of lumen with irregular narrowing from thrombus or  atherosclerosis. Every time I lost the ideal lumen of the vessel. Some solution to it, is shrink-wrap modifier, but to be honest it has big limitation like you mention before. I don't think  that it would handle with dissections either. 

So for that moment, I think we don't have perfect solution to mirror the ideal anatomy of vessel lumen. We can be close, but not accurate.

Maybe Dr. Mike has different opinion?

 

The second aspect is segmentation. What program you recommend ? Osiris or slicer? 

I think that when we use the threshold for Hounsfield units for contrast medium , we also segment part of calcium atherosclerosis which has very big Hounsfield value. Around plaque segmentation see a transition zone which corresponds the value of Hounsfield for contrast medium which we see as very irregular surface. Of course we do smoothing as post processing in blender, however its not dealing perfectly with it. Even if it does, we lose ideal shape of lumen.

So same again, we are close but not accurate.

 

If anybody knows how to deal with these problem, please share with me. 

 

[kopachini]

1 hour ago, froth said:

I am not sure if dealing with solidify modifier is safe procedure. I tried a lot, every time something was wrong. I mean complex geometries of lumen with irregular narrowing from thrombus or  atherosclerosis. Every time I lost the ideal lumen of the vessel. Some solution to it, is shrink-wrap modifier, but to be honest it has big limitation like you mention before. I don't think  that it would handle with dissections either. 

So for that moment, I think we don't have perfect solution to mirror the ideal anatomy of vessel lumen. We can be close, but not accurate.

Maybe Dr. Mike has different opinion?

 

The second aspect is segmentation. What program you recommend ? Osiris or slicer? 

I think that when we use the threshold for Hounsfield units for contrast medium , we also segment part of calcium atherosclerosis which has very big Hounsfield value. Around plaque segmentation see a transition zone which corresponds the value of Hounsfield for contrast medium which we see as very irregular surface. Of course we do smoothing as post processing in blender, however its not dealing perfectly with it. Even if it does, we lose ideal shape of lumen.

So same again, we are close but not accurate.

 

If anybody knows how to deal with these problem, please share with me. 

 

I use 3D Slicer. Try not to use treshold or set it very high, then segment vessel by hand and you manually choose what you want and don't want to segment (in this case you will not segment calcified plaque).

Solution for the dissections, what I can think of right now, would be that you manually segment (select) only vessel wall with a 3 mm circle (pen), and 2 mm circle for dissected intima... but that would be very slow procedure :/

 

Try not to think too much about accuracy because those are submilimeter differences (if your slices are that thin, and I presume that they are  )

 

Again, as I said, outer appearance is not that much important because it only gives you solidity/firmness (it is not recommended to print walls thinner than 1 - 1,5 mm... I usually make vascular models with 3 mm thick walls). The inner sufrace is the one representing your lumen, blood-intima border respectively.

 

I don't have any big problems with solidify modifier/offset in meshmixer. The main problem is the anatomy of the near vessels (circled in pic I posted above) because if they are too close, thick vessel walls (3-4 mm) could overlap, but that is the anatomy of the patient that you can't change (or you can remodel it using Meshmixer or any CAD software, as I did in one model). Solution of that problem would be to merge touching walls.

[Andras Lasso]

For anybody who stumbles upon this thread: we've added "Hollow" effect to 3D Slicer's new Segment Editor module. It has the option of creating vessel wall inside, outside, or around the surface. The method uses labelmap representation for internal computation therefore it is very robust (there are no degenerate triangles or intersecting surfaces in the generated mesh), you may just need to set the resolution of the segmentation if you want to create models of very thin walls..

 

Here is a short demo video about how to use it:

 

We constantly improve 3D Slicer's segmentation capabilities and 3D printing is one of the driving applications, so any feedback or feature requests are welcome.

[Dr. Mike]

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