This was extremely helpful! I bought a CD with my MR images on and now i can now view them perfectly in 3D and that makes all the difference. Big thanx man!
I'll sum up the steps to get a polygon model from DICOM Data. In 3D Slicer. First load Data, and DCM using the top buttons. Click Apply to on GenericAnatomy Colors. Switch Module to Volume Rendering, and click the eyeball by Volume to view the 3D Data. Use ROI to adjust the bounding box. Select Module Model Maker. Under IO load the data. and under ModelCreate new Hirearchy to name your model. Click Apply. File Save and under File Format tab select the Poly Data (.vtk) change to .stl or .ply. STL works in 3DS Max with the correct plug in loaded, also good for Meshmixer and Meshlab. Export to OBJ with an MTL file to get textures. Hope that helps someone This took me a few days to figure out a good process.
Try ZBrush for cleaning up. The fastest way at least. Auto Groups>Remove unnecessary Polygroups>Close Holes. Then... Remesh/DynaMesh or whatever you want.
In the first part, I don't understand why you use the editor to segment and create a label if you don't acutally use that label afterwards when you render the volume. it seems to me you just render the original volume. it's a bit confusing
Thank you for your attention. My name is Pitipong from Thailand . I'm study in Biomedical Engineering bachelor's degree. I am doing a project on Brain Reconstruction. I want to make brain 3d model from MRI 2D picture by mathlab. What do you recommend about the process, theory. Or how to do it? Thank you for your attention. I look forward to your prompt reply. Mr.Pitipong Apisuwankul Thailand
Hi! It took me about 3 weeks to get a good understanding of how the program worked, and what the functions were doing. I use a MBP laptop so it would definitely be faster if you used such a program on a Windows or desktop computer (I compared my experience with my classmates’ and their 3D renderings were processed at a faster rate than mine. I did try Invesalius but they only have a 16bit version for Mac, and that ran really slowly on my laptop. It was easier to use and understand in terms of functionality and tools when compared to 3D Slicer though. AHNTLIA is correct in stating that Invesalius and 3D Slicer are basic and limited tools - as a beginner, I was already struggling with a lot, so this was enough to keep me occupied for a 5-6week period. If you have more time, or a faster ability to adapt to working with such data and tools, then I would agree with AHNTLIA and invest in more expensive software with a larger variety of tools and precision. It really depends on the scope of your project, and what you’re intending to achieve.
Michael Ee Thank you. Appreciate your reply. I most likely will invest in a sophisticated tool since I am thinking of going deep in medical imaging. But I am planning to do that after I learn basics from3D slicer and inVesalius. What were the resource that you used for learning 3D slicer, was it just the tutorials on the wiki page?
Any chance you could explain how to install skullstripper in the current stable version of 3D slicer? Doesn't seem to be a good way (Swiss skull stripper doesn't work)
Bob Janisch Hi Bob, I might not recall how I installed it, but it was an extension that I had to load into the program. I believe there’s an extension manager/preferences sort of dialog for you to find the file, and it should work once you’ve selected it. At least - that’s from what I can remember when I did this last year. Sorry if this information isn’t the most helpful!
Thanks for the tutorial! I'm currently trying to render my brain but is taking awhile.... as a degree student in their final year time is precious, just wondering how long it took to render? Thanks
Good to know there's a lot of amateurs outhere doing it fucking wrong! Meshmixer? 3d slicer? C'mon this applications need good skills and good software. Fortunately this is why this kind of work well done still cost a lot.
Draacid Pay for the knowledge, it's just anoying to have the world fed up of people whot think they can do it all by themselves and trying to make it all free... Buy Geomagic, buy Magics from MAterialise. There you have something constructive.
World_Watcher maybe you want to go for mimics se. 136 USD per student. The real thing must cost around 20000 USD just like magics and similar solutions.
AHNTLIA Thank you for your reply. $20K is indeed a lot of money. But in order to get student edition, I think I must be enrolled in school, which I am not currently. Also MIMICS has two different versions one for clinical use and one nor non clinical uses. I was wanting to have the one for clinical use. However in comparison Invesalious by CTI is free and is intended for clinical use. Let us see I am planning to install all 3 (MIMICS, Invesalious and 3D slicer) and compare them all. I request you to let me know if you have already compared them.
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This was extremely helpful! I bought a CD with my MR images on and now i can now view them perfectly in 3D and that makes all the difference. Big thanx man!
I'll sum up the steps to get a polygon model from DICOM Data.
In 3D Slicer. First load Data, and DCM using the top buttons. Click Apply to on GenericAnatomy Colors. Switch Module to Volume Rendering, and click the eyeball by Volume to view the 3D Data. Use ROI to adjust the bounding box.
Select Module Model Maker. Under IO load the data. and under ModelCreate new Hirearchy to name your model. Click Apply.
File Save and under File Format tab select the Poly Data (.vtk) change to .stl or .ply. STL works in 3DS Max with the correct plug in loaded, also good for Meshmixer and Meshlab. Export to OBJ with an MTL file to get textures.
Hope that helps someone This took me a few days to figure out a good process.
This is exactly what i was looking for, thx so much! A really helpful and fun video.
Fantastic information. Thank you.
HANDSOME AND INFORMATIVE :D
This is excellent!
Hi Mr Ee, I am from ML101!!! Haha, nice video
Try ZBrush for cleaning up. The fastest way at least.
Auto Groups>Remove unnecessary Polygroups>Close Holes. Then... Remesh/DynaMesh or whatever you want.
hi,
I am new to slicer. It seems none of the "preset " is working for my CT images. I have a mice CT data in which I need to measure the tumor size
In the first part, I don't understand why you use the editor to segment and create a label if you don't acutally use that label afterwards when you render the volume. it seems to me you just render the original volume. it's a bit confusing
Thank you for your attention. My name is Pitipong from Thailand . I'm study in Biomedical Engineering bachelor's degree.
I am doing a project on Brain Reconstruction. I want to make brain 3d model from MRI 2D picture by mathlab. What do you recommend about the process, theory. Or how to do it?
Thank you for your attention. I look forward to your prompt reply.
Mr.Pitipong Apisuwankul
Thailand
Do you happen to know how to go from DICOM MRI to stereoscopic file for Google Cardboard viewing?
there is no save .STL in my last version of Slicer...wtf?
Nice! Thank you. This is what I was looking for. How long did it take for you to learn 3D slicer and what resources did you use?
Hi! It took me about 3 weeks to get a good understanding of how the program worked, and what the functions were doing. I use a MBP laptop so it would definitely be faster if you used such a program on a Windows or desktop computer (I compared my experience with my classmates’ and their 3D renderings were processed at a faster rate than mine.
I did try Invesalius but they only have a 16bit version for Mac, and that ran really slowly on my laptop. It was easier to use and understand in terms of functionality and tools when compared to 3D Slicer though.
AHNTLIA is correct in stating that Invesalius and 3D Slicer are basic and limited tools - as a beginner, I was already struggling with a lot, so this was enough to keep me occupied for a 5-6week period. If you have more time, or a faster ability to adapt to working with such data and tools, then I would agree with AHNTLIA and invest in more expensive software with a larger variety of tools and precision.
It really depends on the scope of your project, and what you’re intending to achieve.
Michael Ee Thank you. Appreciate your reply. I most likely will invest in a sophisticated tool since I am thinking of going deep in medical imaging. But I am planning to do that after I learn basics from3D slicer and inVesalius. What were the resource that you used for learning 3D slicer, was it just the tutorials on the wiki page?
can u please give a tutorial for printing 3d unborn baby? thx b4
Any chance you could explain how to install skullstripper in the current stable version of 3D slicer? Doesn't seem to be a good way (Swiss skull stripper doesn't work)
Bob Janisch Hi Bob, I might not recall how I installed it, but it was an extension that I had to load into the program. I believe there’s an extension manager/preferences sort of dialog for you to find the file, and it should work once you’ve selected it. At least - that’s from what I can remember when I did this last year. Sorry if this information isn’t the most helpful!
Thanks for the tutorial! I'm currently trying to render my brain but is taking awhile.... as a degree student in their final year time is precious, just wondering how long it took to render?
Thanks
It was quite fast (no more than an hour) for me.
Michael. Can I pay you to give me some lessons on teamviewer?
Good to know there's a lot of amateurs outhere doing it fucking wrong! Meshmixer? 3d slicer? C'mon this applications need good skills and good software. Fortunately this is why this kind of work well done still cost a lot.
add something constructive for betterment of all
Draacid
Pay for the knowledge, it's just anoying to have the world fed up of people whot think they can do it all by themselves and trying to make it all free...
Buy Geomagic, buy Magics from MAterialise. There you have something constructive.
AHNTLIA Since you know quiet a bit about this, do you have any information as to how much Materialise MIMICS cost? Thank you.
World_Watcher maybe you want to go for mimics se. 136 USD per student. The real thing must cost around 20000 USD just like magics and similar solutions.
AHNTLIA Thank you for your reply. $20K is indeed a lot of money. But in order to get student edition, I think I must be enrolled in school, which I am not currently. Also MIMICS has two different versions one for clinical use and one nor non clinical uses. I was wanting to have the one for clinical use.
However in comparison Invesalious by CTI is free and is intended for clinical use. Let us see I am planning to install all 3 (MIMICS, Invesalious and 3D slicer) and compare them all.
I request you to let me know if you have already compared them.