Tutorial: Ct scan to 3D print in 15 minutes using free software only.
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- เผยแพร่เมื่อ 28 เม.ย. 2018
- Video tutorial to process CT data and make it ready for 3D printing. Whole process should take 10-15 minutes, and only uses free software. Apologies for a few areas of de-sync between audio and video - work laptop struggled to handle screen recording and 3D software with dignity!
Links:
My website (with non-video tutorial): pfalkingham.wordpress.com/201...
CrocBase CT data: osf.io/6zamj/
3D Slicer: www.slicer.org/
Ultimaker Cura: ultimaker.com/en/products/ult...
Dremel Plugin: github.com/timmehtimmeh/Cura-...
If you found this video useful, I wouldn't say no to a coffee!: www.buymeacoffee.com/pfalkingham - วิทยาศาสตร์และเทคโนโลยี
Which characteristics have that computer that are you using?
For this video, I'm using my Dell m3800: 16gb ram, 4 core i7 haswell and an nvidia quadro m1100.
@@PeterFalkingham Mmmmm, ok, thank you! Becasuse I'm using an Asus X541UJ, with 8gb ram, intel i7, and Nvidia Geforce 2gb and it has problems... But what i'm trying to visualize is a CTscan of 1800 slizes, so maybe that's the problem... I was thinking in increase the ram memory to 16, and let's see if it works better...
@@miguelangelmoreno.8581 sounds like data from microCT? I've had issues with large datasets in Slicer too. I've ended up using meVisLab to crop data before visualizing. I also want to try dragonfly on microCT data. See my latest blog post for other free software options.
@@PeterFalkingham ok, thank you very much. The good point that i saw in Slicer was that it's free, and easy to learn (at least for what I need to do)... I will check the blog to see more options.
@@PeterFalkingham For now, at least, microCT is the formar what i will be working with... So, I've seen in your blog different good options... But, haven't you try any of them with microCT (just in case you could recommend me one or other for this...). In any case, and above all, thank you for answering!
Hello, i'm trying to use this software with a microCT scan of a human archaeological cranium, but my computer collapses... How many slizes have that model that you use in the video? Because mine have 1800.. I'm using in a portatil computer Intel Core I7, with 8Gb RAM memory... I don't know if my computer hasn't enough strenght or if i'm trying to load too much slizes...
Yeah, I've had issues with 3d slicer crashing with large microCT datasets. If you check out my latest blog post, I've discussed a range of other softwares. For microCT I ended up using mevislab and cropping before visualising, but it's not an easy software to learn. I may try testing them all with a microCT dataset at some point, but as I don't usually work with such large datasets it's a case of finding the time.
Great tutorial.Thanks¡
Thanks a lot, this is a great video! It is good to see how the features that we develop get used (and here they are used very well).
I have a few recommendations that you might find useful:
1. I've just noticed that you set slice position separately in each view - you may use Shift + MouseMove to move crosshair (and by default that moves all the slices to the current position) in either slice or 3D view. You can customize how the crosshair is displayed using the crosshair button on the toolbar.
2. You may use Scissors effect to remove irrelevant parts by drawing in either slice or 3D views.
3. In recent nightly versions, we have greatly improved 3D update speed, the only smoothing step is still slow. If you disable smoothing (set smoothing factor to 0 in the dropdown menu of "Show 3D" button) then 3D updates should be a magnitude faster.
Looking forward to see more tutorial videos!
Thanks!
1. Ah, that's good to know, thanks.
2. Yes, that one I was aware of, but here the joins were quite awkward (just a couple of voxels each) and the eraser tool was a bit quicker.
3. Ah, just tried it now - miles faster, thanks!
This was extremely helpful! Thank you for putting this info out there!
ah cmon, this crap isnt working anymore (website)
hey all my ct scans are either in jpeg or htm any idea how I could make this work?
Htm stack sounds weird, I've never heard of that, but a jpg stack opens in slicer exactly the same way as in this video.
Wow, this is great. Thank you for taking the time to share this.
I have a Calcaneal implant after shattering my heel (or Calcaneal).
How would I isolate the the implant from my foot CT (nrrd) and vice versa so I can model them both individually?
I've managed to kind of do this in the volume rendering, but not in the segment editor as the implant is screwed in.
Presumably the implant is a different density to your bone? If so, you set the threshold differently (sounds like you've done this in the volume rendering) - you just use those same thresholds when adding the labels, then convert each to a separate model.
It worked with me, but with the files I have I feel like it is kind of a wonder that the program really knew what pictures it should take if import the files from a certain hospital. If I try to do the same from a different foto set from a different hospital I can not seem to get the corresponding images together.
If it's not recognizing your image stack, then presumably the metadata is missing, and you need to tell it pixel and slice distances. You'd get that from the original scanner.
@@PeterFalkingham Is there a way to know if i have the metadata? or is it embedded into each file?
@@nolschaars7048 Sometimes it's a separate file
fantastic
having my ribcage 3-d printed and the image with the cartilage is separate and can't be printed with the ribs or without the other softer stuff in the image. Any tips?
There are very complex ways of doing it, but not the kind of thing I could help with. I'd make models from the bone CT and cartilage CT, then align and merge them in Blender or such before 3D printing.
Hi, Thanx for the video recording. How precise will 3D slicer be for my dicom data if I need to separate the pores from the grains for micro ct scanned rock sample? Please help me with this. My data is around 60GB and I trust my computer with 64GB RAM and a sophisticated graphics card should be able to handle this. I need to print the pores and the grains separately, I appreciate any help in advance.
3D Slicer will be as precise as your data - there's no issues there. Your machine should handle the data fine, but I've found 3D slicer to struggle a bit with MicroCT (it can be quite slow). I prefer using Dragonfly (free for academic use, see here: peterfalkingham.com/2019/02/18/free-software-for-ct-segmentation-2019/ and here: www.theobjects.com/dragonfly/).
@@PeterFalkingham Thanx so much for the idea. I'm checking Dragonfly right away. Cheers.
Thanks a lot! Huge fan of your work on kingfisher hydrodynamics.
Is there a way I can fill up the 'holes' in my segmented structure without manually painting each slice? Does Slicer offer a feature like this?
Yes, you can - there's a fill holes button that works in 2D (per slice) or 3D.
hello, do you have hand and finger dicom file? I need It, wold you please send it to me if you have??
I don't, sorry.
Hi, thanks for your tutorial.
I'm having trouble finding the most important step of the video and that's saving it as a STL file.
I've tried exporting as that's the only place where I see the word 'STL' but it isn't working. Pressing export gives no response.
When I press save on the other hand, STL does not appear as a save option.
I'm unsure how you did it really.
I'm trying to convert a DICOM file of a baby face into a STL.
Do I have to perform segmentation for it to work? I was hoping to just immediately convert the file to STL?
Much appreciated. You are perhaps the only guy on TH-cam explaining this so I'm grateful.
Thanks
Hi - yes, you have to segment first, for the export as stl to be available. It doesn't know where to separate between what you want (the face) and what you don't (all the space around it, internal structure etc) until you've segmented it.
Once you've done that, the ability to save as an STL will be available in the save dialogue.
@@PeterFalkingham
Thank you very much Peter. I'll give it another try.
I wish you the very best.
very easy and fast thank you for this.
although i found i can print bones, i cant see the information i wanted on soft tissue
Do you just need to change the threshold values? Or is the problem with the scan - Normal CT can be quite poor for distinguishing soft tissues; either iodine staining or MRI are better.
非常感谢，我尝试着打印出患者的下颌骨，可以用来做种植牙手术规划。
I am not understanding, I dont have any "ct" file, I have a .vol file. What should I do?
I don't think I've come across .vol files before. Normal CT files are .dicom, or .tif once processed by the CT machine's software. It might require proprietary software, or you might be able to open it with something like Paraview.
How save file to stl?
Exactly as it describes in the video @11 minutes - I saved out to stl in the video.
Nice video! I've recently been linked to your blog via researchgate and I've got a question:
I need to reconstruct the reproductive tract of (glands, gonads and associated structures) whip spiders for my master thesis and have CT data available for the entire opisthosoma. So I basically need to get a 3D model of a CT image stack. It was planned to reconstruct the reproductive system via Fei Amira, but I only have access to it a university PC and I have to travel for like 1.5 to 2 hours to go there. So my question is if 3D Slicer would also be capable of performing the required tasks similar to Amira? My home PC is fairly decent and if I could actually do this at home, it will probably dramatically speed up the process and save me loads of time! Thanks in advance!
Yes, 3d Slicer could probably do it just as well as Amira, but my current go-to software is Dragonfly (www.theobjects.com/dragonfly/) - I'll be doing a tutorial on that soon if I can get chance. Eitherway, the free alternatives can do everything Amira can, providing you've a decent computer at home.