Hi,
I am trying to learn how to convert CT Scan files into CAD geometry which later I can use for flow simulation.
I looked on the internet and downloaded trial versions of software like Mimics, 3-D Slicer and 3D Doctor. After importing the DICOM files, converting them into CAd file as a whole is pretty easy but issue with my work is that I need to take out artery and vein at one particular part.
I have absolutely no idea what should be the threshold value for that portion and me being from an engineering background and not from medical is making it more tough for me.
Any suggestion or help is highly appreciated.
Dear Mishra,
As mentioned above by Mico Stanojevic, I would also recommend you the Simpleware software suite. You can download a trial version from http://simpleware.com/software/trial/ just to see how it works. After you install the trial version you'll gain access to the users guide where you can find a very useful tutorial about the blood vessel reconstruction and mesh generation. I would also kindly advise you to visit the official Simpleware's Youtube Channel at https://www.youtube.com/user/simplewareuk for a quick reference.
I attached to this message one of my papers regarding the image based reconstruction of a blood vessel network that was used as computational domain in a pulsatile blood flow-vessel interaction numerical study. I hope it will be of use.
3D slicer is a very good software but it's very difficult to be used.
I suggest you to use Rhynoceros 3D in order to traslate the DICOM file in a CAD-MESH.
The CAD Mesh can be used to be remeshed or to create a surface (A-class) model.
If you need any help with your file I can ask to one of my PhD students to translate it for you. Let me know
In 3D slicer in built threshold value are given for different bones, blood vessels Have seen it
In 3D slicer while performing cropping operation you ll find a "shift "option which looks like volume tab windows media player .You can adjust the threshold value there.
why not save them in different files and import separately into your FE software?
what is your FE software?
Dear Mr Mishra,
It depends on various factors. If you are focused on custom made implantation , maybe it had better to use hybrid approach of modeling. For example, in CAD software like SpaceClaim or CATIA with adequate modules, one may combine stl mesh and its make editing in assembly (it allows high topology complexity), and custom parametric CAD modeling of implants.
The other well known CAD software has serious problems like SW, Inventor to achieve such stl importing approach (intensive processing time consumption with non-robust model).
As the first step, generation of stl mesh of some biomedical models through 3D CT reconstruction, Mimics is well known, but also there is a very robust and fast software like ScanIP by Simpleware with useful modules for FEA meshing. I have very good experience with it.
If one investigate FEA modeling of biomodels and their load / CFD simulations etc, indirect "CAD" conversion" should be avoid if possible. In ScanIP with +FEA module, after primary 3D reconstruction (image processing and filtering), masking, you can convert very fast these models directly into adequate FE mesh, for MSC Patran, Nastran, Abaqus, neutral... with selection of mesh size, adaptive approach, evenmore you can make nonlinear material models, etc.
In general, conversion from stl into common CAD stp/step or igs/iges formats should be avoid, especially for organs/anatomical structures with high complex topology.
Such conversion has sense, if one make hybrid model together with stl surface model of organ in assembly with cad regular model of implant, but with kept problems of editing. It is good just for testing of assembling and certain fitting/overlapping.
In my opinion, the best combination of programs is Mimics/3matic/Geomagic. Mimics is good for going through the slices, 3matic is good for remeshing and creating a solid mesh, and Geomagic is good for editing the surface files used to create the solid mesh. I also use Amira/Avizo, but editing the surface volumes is a little more difficult here.
As for the threshold, it will depend largely on the resolution of your scans, whether a filter was used, the quality of the scanner itself, and the settings of the scanner. E.g. the microCT scanner we use in my lab produces really sharp images with a copper filter when the filament is new, but as the filament gets older, the resolution of the images goes down and we need to change the settings.
Likely, you will have to do some slice by slice editing to get the model you want and it will not be as simple as thresholding a set of scans
Dear Mishra,
As mentioned above by Mico Stanojevic, I would also recommend you the Simpleware software suite. You can download a trial version from http://simpleware.com/software/trial/ just to see how it works. After you install the trial version you'll gain access to the users guide where you can find a very useful tutorial about the blood vessel reconstruction and mesh generation. I would also kindly advise you to visit the official Simpleware's Youtube Channel at https://www.youtube.com/user/simplewareuk for a quick reference.
I attached to this message one of my papers regarding the image based reconstruction of a blood vessel network that was used as computational domain in a pulsatile blood flow-vessel interaction numerical study. I hope it will be of use.
There is another package that we have used for segmentation and surface mesh extraction that is done by Volume Graphics called VGStudio Max https://www.volumegraphics.com/en/products/vgstudio-max.html that can do a segmentation and surface extraction in only 2-3 steps. The soft ware was designed for CT metrology applications but also imports dicom files and raw files as well an. Depending on the dataset I've segmented and exported STLs in less than 2 minutes with it. Its expensive but you can also get a demo license for it that works for this purpose.
Hi ,
VMTK lab is also interesting http://vmtklab.orobix.com/, you can request a demo version , it's also not very expensive and simple to use .
Good luck .
ITK-Snap will work fine for creating STL models from CT scan images (DICOM file).
The latest version of Avizo (9.4) provides the complete workflow to do segmentation and to quickly create accurate volumetric mesh (not just surface mesh) without the need to do any editing. Avizo can even export the mesh in Ansys, Abacus, Comsol or Fluent etc proprietary formats (in addition to STL format)
More info is available at https://www.fei.com/software/amira-avizo-meshing-for-fea-cfd/
Assuming you can still export a surface to stl in an evaluation version of VG I agree with Azzaz. If you can't then use something like mimics / geomagic (commonly used in biomechanics) or matlab to FIJI (imageJ) to threshold and export as an stl. However its usually a very quick process in VG.
I hope Its fisrt better to work with 3D doctor, 3D Slicer for awareness of Exact awareness on Problem of study.
1. First collect all 3 view images of your interset from medical research centre.
2. Then go for exact selection of ROI (Region of Interset) in the 3 views.
3. Next try to reconstruct it with available segmentation in the chosen tool.
5. If you are a mechanical guy you can use autodesk for better and accurate model.
6. Then import it to Fluent for Flow analysis.
Lot of Videos for awareness on various tools to work on. '
Make your own framework according to suggest the best way of analyzing your interested problem.
All the best for further endeavors.
Dear mishra ji,
Its a 5 year back question. If its unsolved the following points may give an idea
1.Then its better to use 3-matic to choose your desired Region Of Interest (ROI).
2. Change your view of region of interest to get your exact part rather than thresholding method. Use any other segmentation method apart from thresholding.
3. Import that STL to any other FSI for your desired analysis usually it may be stress and pressure analysis to know dysfunction of the abnormal vein.
I hope your ROI is a study of FSI (Fluid Structure Interaction) to incorporate things of coupling.
4.You can get many opensource FSI tools to continue your work.
5. Otherwise using any slicer tool make a 3D printed part withv solvents.
6. ITK snap is another good option for choosing your vein.
All the best for our future endeavours.
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