A straight-forward DICOM to STL conversion is easily possible with 3DSlicer, an open-source software tool that you can download here: http://www.slicer.org/ .

Your question has been answered as well in the FAQ section there:

- use the File/Add Volume module to load the data into Slicer

- use the Interactive Editor to create a label map which contains the structure you are interested in

- use the Modelmaker functionality to create a triangulated surface model

- use File/Save to save the model in STL format.

You can do this by using a couple of Freeware tools. ITK-Snap ( http://www.itksnap.org ) can read in the DICOM files and with some image manipulation using the built in segmentation tools you can get a surface hull. These can be imported into Meshlab ( http://meshlab.sourceforge.net) to generated an STL file.

To convert DICOM to DXF or WaveFront files (not STL), is is possible to use the '3D viewer' in ImageJ: http://rsb.info.nih.gov/ij/

A straight-forward DICOM to STL conversion is easily possible with 3DSlicer, an open-source software tool that you can download here: http://www.slicer.org/ .

Your question has been answered as well in the FAQ section there:

- use the File/Add Volume module to load the data into Slicer

- use the Interactive Editor to create a label map which contains the structure you are interested in

- use the Modelmaker functionality to create a triangulated surface model

- use File/Save to save the model in STL format.

Check out

www.mevislab.de (which is a graphical programming 3D image analysis framework that also wraps VTK and ITK)

and look in the documentation for modules writing STL data formats

Hi Volker,

Thanks for your reply. Would it be possible for you to send me an mlab file that does this?

Kind regards,

Peter

MIPAV (Medical Image Processing and Visualization )is open source tool to extract any single slice or to find slice average (surface representation in your case) from DICOM dataset.

Have you tried Osirix? It's Mac based but it takes in DICOM, 3D models and then you can export as a surface STL. It's free and very robust. Check it out if you haven't already done so.

You can find many software links and descriptions in this link:

http://www.additive3d.com/sw07_lks.htm

You can also see SPM (Statistical Parametric Mapping) Software

You can use ITK

Hi Peter van Ooijen,

Although the post is quit old and you might have figured out the solution, I am writing for others who have the same problem. In MeVisLab, you can look at the example of WEMIsoSurface. In the search module write WEMIsoSurface and then right click the module and select "Show Example". You will get the complete mlab network, where you can set the minimum and the maximum iso value to get the surface representation. You can smooth out the surface with WEMSmooth or save the surface with WEMSave in STL or other formats. If there is any module just right click and select "Show Example Network" and you will get an example network for that module.

The platform independent application MITK Workbench, built upon the medical imaging interaction toolkit (MITK), is a lightweight tool for such purposes (DICOM import, segmentation, mesh generation, volume visualization, etc.).

http://www.mitk.org

Of course for some kinds of data (e.g. MRI merged from several partial scans) it may still require the operator to manually correct the initial 'guesses' of the algorithm. This strongly depends on the input data type, the structures that you wish to segment and the surface accuracy required.

hi Peter

import your dicom data into a free ware 3Dslicer.

segment the required part from it an then save it as a model in stl format.

Both model making & saving in stl format can be done in 3D slicer only.

regards

aakash

Dag Peter,

Je kan invesalius proberen. Het heeft dezelfde lay out en workflow als mimics van materialise en werkt perfect. Met behulp van dit programma heb ik al een hele hoop stl-files gegenereerd. Zeker een aanrader.

http://svn.softwarepublico.gov.br/trac/invesalius

Groet Maarten

Beste Maarten,

Bedankt voor de tip, ga dit zeker even proberen (de download is nu bezig).

groet,

Peter

Hi Peter

The surface rendering module of Osirix ( http://www.osirix-viewer.com ) is capable of STL output. Segmentation is relative straight forward. Cave: OSX only!

From the commercial side I recommend Amira

( http://www.vsg3d.com/amira/overview ) for advanced segmentation tasks. Although its a commercial package, there is a time-limited evaluation version available.

ps: Did not check Summers recommendation. Sorry for duplication!

Use 3d Doctor, freely available.

Dear Peter, the software developed by my company Simpleware is suitable for this task - please see www.simpleware.com for a free 30-day trial.

Use 3D doctor freely available.

Use Amira And Mimic Paid versions.

One of the best choices is osiriX, it is a free mac based software. No matter what software you use for this conversion, it is highly recommended that you fix and "refine" your STL wit a CAD software afterward. 

I succesfully used the following steps, to make a 3D brain phantom from MR DICOM data:

• Used Devide, where I created a script for filtering and transformations (contact me if you want the script).  There is a youtube film somewhere which gave me a head start - sorry don't have the link anymore.
• I used Devide both for whole brain, and for a number of internal structures which were 3D-printed separately
• Tested the files in MeshLab
• Used meshmixer to fix things
• Then I had professional help to making a lid, add flanges, etc in software.

Hope this helps

I find Mimics materialise the easiest to use but at a certain cost. I would say it depends on your budget. 3D slicer is good, but the segmentation process is tricky. If it is just volume rendering and from there getting an STL file Osirix is great too.

InVesalius is designed to do this job.

http://en.wikipedia.org/wiki/InVesalius

Mayo Clinics ANALYZE software is a commercially available software for segmentation and conversion of DICOM data to STL.  Like MIMICS, it is quite expensive.

Try the free version of MeVisLab available at

http://www.mevislab.de/

It offers a bunch of segmentation and visualization tools and will allow to store segmentation results in STL beside many other formats.

You will need to work through some tutorials to make good use of it, as is a tollbox rather than a program to do a patricular job.

But very efficient segmentation and quantfication software was build based on it.

The free MeVisLab version comprises warppers for graphical programming with  most ITK algorithms.

A comercial license is required to build more complex software requiring e.g. python scripting to implement more complex workflow automation.

how to convert fro stl to dxd file?

did you mean stl to DXF (not DXD) file?

for that purpose i recommend Blender (http://www.blender.org/)

try ;)

Bruker provides its software CTan (along with CVol) as a demo version. It is about 5 mb and very easy to install. After installation (i) open your Dicom data using File > open. (ii) click on binary selection preview and then click on from data set. (iii) now click on create 3D model and save as .stl format.

This .stl format can be viewed using CVol.

http://bruker-microct.com/products/downloads.htm 

You should definitely try Dornheim Segmenter, it has been designed specifically for creating 3D models (STL and many more) from medical scan data (e.g. DICOM).The software is very easy to use and you can download a free version here: www.dornheim-segmenter.de/en

For a quick overview have a look at https://www.youtube.com/channel/UCb-YtwJlzR3yw2QYgTva-2w

You can try my software Real3d VolViCon that takes a single volume file or a sequence of 2D (i.e., DICOM) files and reconstruct the 3D volume (voxels) as well as mesh (surfaces) models. Have a look at http://real3d.pk/volvicon/

For 3D Meshes such as STL, PLY, OBJ, try Real3d Renderer at http://real3d.pk/rend.html.

You can use VTK. It generates 3D isometric surface from MRI scans with the help of Marching Cubes algorithm and can save it in .STL format.

We've made huge improvements in 3D Slicer's segmentation features. It's free software and it has many features that even expensive proprietary software don't have. Here are a step-by-step tutorials that explain how to create models of various structures: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Image_Segmentation

If you have any questions or suggestions for improvements then you can post it at https://discourse.slicer.org.

Our Checkpoint software can load DICOM, perform 3D rendering, and also export STL surfaces from CT scans and other volume data. It also has several tools built-in to perform 3D shape analysis if that's something you're also interested in.

https://www.stratovan.com/products/checkpoint

I recommend Andras's answer

Best Regards

I currently used ivesalius (brazil) and seg3d (university of Utah-US) and i think seg3D is better (not sure if Drishti -australia can export the segmented model in stl)

(the whole process is relatively easy: import data (dicom files) apply threshold or other for choosing the area of interest- construct iso surface -export isosurface as *.stl)

You can use the Brasilian invesalius software. Its free.

Peter Van Ooijen

I use 3D slicer works very fine with DICOM data from CT scans. But I run it on a PC computer. I had many problems with Mac computers. https://www.slicer.org/

Many people use 3D Slicer on Mac without problems. If you can report any issues or ask questions related to 3D Slicer at https://discourse.slicer.org - you'll get answer within hours.

Use Miele-LXIV to export to an .stl file: https://itunes.apple.com/us/app/miele-lxiv/id988332475 see http://i.imgur.com/7CzHupN.jpg

3D slicer or

u can use of itk and vtk tools in c++ and write a program to do it

for a totally free approach someone can also use fiji (imageJ)

a routine could be:

Make a stack from dicom files (Import sequence) , (set scale if necessary -most probably dicom has already the correct information about scale and z axis length of slices), adjust it accordingly (sharpen , contrast/brightness etc) segment the stack IF you wish with Trainable Wekka segmentation plugin (for instance, other segmentation processes may also work), then use 3d viewer plugin to convert it in 3d (surface) adjust the threshold and if the result is suitable for your demands, export it from 3dviewer as stl dxf or other option ..

good lack

agreed 3D slicer