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Converting 3d ultrasound images to stl/obj

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Posted · Converting 3d ultrasound images to stl/obj

Bonjour,

Let me jump in...

Because of the way the images are generated, 3D ultrasound data have voxels that are expressed in a spherical system. DICOM (as it stand now) only support voxels in a Cartesian system.

So the manufacturers have a few choices:

- They can save the data in proprietary format (Kretzfile for Ge, MVL for Samsung) .

- They can save the data in private tags inside a DICOM file (Ge, Hitachi, Philips)

- They can re-format the voxels to be in Cartesian, but then the data has been transformed and nobody like that. And anyway, since they also need to save the original (untransformed) data, the companies that do offer Cartesian voxels, usually save them in the same way as the original, so they are not saved in normal DICOM tags, but in their proprietary version.

So most of the standard software that can do 3D from CT or MR will not be able to cope with the data files. (Let alone the fact that ultrasound datasets are inherently very noisy!)

I do have a product that will read most of the 3D ultrasound files and create an STL model directly from the datasets (spherical or Cartesian). It is called "Baby SliceO": http://www.tomovision.com/products/baby_sliceo.html

Unfortunately, it is not free, but you can try it without any licenses. Give it a try and let me know if you like it...

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Posted · Converting 3d ultrasound images to stl/obj

It's an old post, but it may still be useful for some people.

If you can get the image to show on a computer, the simples solution may be to make a screendump, save that as JPG-file, maybe clean it up in Photoshop or Gimp, and try to import that JPG-file in Cura.

Another solution could be to make a photograph from the screen (e.g. at the doctor), or make a scan or a photo of a röntgen or of similar transparant slides.

Then you don't need any conversion software.

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Posted · Converting 3d ultrasound images to stl/obj

It is possible.

It is the source file settings on the machine during the export process and you need segmentation software. It must have great edge detection. Just because the data is there is does not mean that the software will auto-detect the true surface and make the complex mesh surface. Not to mention the quality of the scan is critical.

The issue with MRI is the contrast normally is poor between tissue types. But the difference in the density of the fluid and skin is great enough it would be easy.

Connect with me on LinkedIn, some of the details on the similar project can be found there.

https://www.linkedin.com/in/ken-yielding/

Ken13244640_10207182943078113_3523966545618600771_n.thumb.jpg.27c7b1cf273e28d413b001d8c6a54679.jpg

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Posted · Converting 3d ultrasound images to stl/obj

I've implemented a GE/Kretz 3D ultrasound image reader in 3D Slicer. After you have loaded the image you can use all the awesome tools in 3D Slicer to visualize and process it (for example, to create a 3D-printable model). You can see a demo here:

It's not perfect yet (spherical to Cartesian conversion is not fully accurate), but it's completely free and open-source - fixes and improvements are welcome. For further details and questions please post to the 3D Slicer forum:

https://discourse.slicer.org/t/loading-of-ge-kretz-ultrasound-volumes-vol-file/808/14?u=lassoan

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Posted · Converting 3d ultrasound images to stl/obj

I am doing it with materialise mimics but I would really like to do it with open source software.

adeelamalik send me an email or something to send you dicom ultrasound data.

Hello antoniosmd, you can help me, sending an ultrasound unborn baby, I would appreciate it very much.

wilberlt@gmail.com

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Posted · Converting 3d ultrasound images to stl/obj

I am doing it with materialise mimics but I would really like to do it with open source software.

adeelamalik send me an email or something to send you dicom ultrasound data.

Hi antoniosmd, you can help me plz, sending an ultrasound unborn baby, I would appreciate it very much.

wilberlt@gmail . com

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Posted · Converting 3d ultrasound images to stl/obj

Dear friends, I was offered to buy a Medison Accuvix XQ (like this one http://www.ultrasolutions.com/medison-accuvix-xq-ultrasound-machine).

Will I be able with that utrasound machine, to print the fetus with a 3d printer?

I think the volume output file will be .mvl...

Please help me out...the price is good but I need to know if I will be able to 3d print the resutls...

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Posted · Converting 3d ultrasound images to stl/obj

You need to ask them what file formats it can save the 3D and 4D images into. If they just say "DICOM" it is not enough, as often 3D data is saved into private DICOM tags, which can only be interpreted by proprietary software, so you cannot load it into 3D Slicer or other software that segments the image and writes to STL. Probably the best is to ask for sample 3D and 4D files that the device can export. If you share those sample files with me I can check if they are usable.

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Posted · Converting 3d ultrasound images to stl/obj

Bonjour Giovanni,

 

Indeed the Accuvix will export the 3D/4D data in ".mvl" (Medison Volume) format.  The data inside these files can be either spherical or Cartesian.  MVL is not DICOM or even a variation on DICOM.  It is a proprietary format developed by Medison.  Actually there's 2 variation of the MVL format, the one used by the Accuvix I call "version 221" is a lot more complex than the "old" variation.

 

You can see a list of the 3D ultrasound file format I have encounter up-to-now on my web site:

http://www.tomovision.com/products/format_image.html

 

Also, do not forget that 4D files usually have a lower resolution than 3D.  So if you want to do models from the datasets, you are better with the 3D.

 

Yves

 

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Posted · Converting 3d ultrasound images to stl/obj
46 minutes ago, Y_Martel said:

Bonjour Giovanni,

 

Indeed the Accuvix will export the 3D/4D data in ".mvl" (Medison Volume) format.  The data inside these files can be either spherical or Cartesian.  MVL is not DICOM or even a variation on DICOM.  It is a proprietary format developed by Medison.  Actually there's 2 variation of the MVL format, the one used by the Accuvix I call "version 221" is a lot more complex than the "old" variation.

 

You can see a list of the 3D ultrasound file format I have encounter up-to-now on my web site:

http://www.tomovision.com/products/format_image.html

 

Also, do not forget that 4D files usually have a lower resolution than 3D.  So if you want to do models from the datasets, you are better with the 3D.

 

Yves

 

dear Yves,

Thank you for your reply. So have you had direct experence of a file mvl generated by a Medison Accuvix XQ? do you that I will be able to 3d print them with your software Babyslice0? 

I was offered to but a Medison Accuvix XQ, do you think I can safely buy it, knowing that then I will be able to print the volumes with your method, no matter what type of mvl file will I get?

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Posted · Converting 3d ultrasound images to stl/obj

Bonjour Giovanni,

 

The short answer is: yes, the software will enable you to make 3D STL models from your data-sets.   

 

You will be able to load the models, in any variation of the MVL format, with either Cartesian or spherical voxels (you are better to export in Spherical an let my software re-slice the data).  The software will also enable you to edit the model to remove any ultrasound artefacts, either directly on the screen, or in VR with an Oculus Rift headset (and that is at least 10 time faster!)

 

In the FAQ section of my web site there's some info on how to save the volumes on Ge and Samsung systems.

 

But I don't want to go in to much details here, these kind of forums are usually not the place to discuss commercial products...

 

If you want more information, I would suggest you contact me directly at martel(at)tomovision.com.

 

Yves

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Posted · Converting 3d ultrasound images to stl/obj

Yves, can your software export volumes to open research image file formats such as nrrd or mha? That would allow segmentation and model generation using cutting-edge open-source tools, such as 3D Slicer's Segment Editor, or ITK-snap.

 

3D Slicer can also do virtual reality visualization of data sets, not just 3D but 4D as well, using HTC Vive, Oculus Rift, and any other Openvr-capable headsets, even without segmentation - using direct volume rendering, you can combine models with imported CAD models, etc. So, export is really important, if somebody needs sophisticated processing, visualization, or analysis. 

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Posted · Converting 3d ultrasound images to stl/obj

Bonjour Iassoan,

 

I'm afraid my software does not export in one of these formats.  But is does save the volume in a very simple format (a simple ASCII header, followed by the voxels in 32 bits IEEE float) so a converter would be easy to do.  Actually I have a few university clients who use the software only as converter to be able to access the proprietary spherical ultrasound datasets created on Ge and Samsung scanners in their research projects...  I was not aware of nrrd, but looking at it, it is very similar to what I do!  So I guess I should also offer an export in that format :)

 

Now I understand that other software also do VR visualisation, but what I do is actually edition of the volume in VR.  When I first wrote that VR module, to be honest, I though it would be a gadget...  until I actually used it!  Doing the edition of a volume in VR is so much easier than on a 2D screen.  The stereoscopy of these goggles is so good, you have the model a few inches in front of you and you sculpt it directly in 3D... Of course maintaining 90 fps needed for good VR is a bitch, that's why the software only run on computer equipped with Nvidia graphic cards (I do almost all the computation inside the GPU).

 

Yves

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Posted · Converting 3d ultrasound images to stl/obj

Yes, nrrd format has a variant consisting of a simple text header file (.nhdr) that describes the image geometry, voxel scalar type, etc., and a bulk data file (.raw) that contains voxel values. NRRD readers/writers area available in all medical image computing software and toolkits that I know of, so it should be enough to have this single export file format.

 

We have very similar experience with VR. It's not just that it provides wall-sized, immersive stereo display, but it also allows directly grabbing and manipulating objects as in the real world. It can actually replace 3D printing in many use cases (but probably Ultimaker forum is not the best place to discuss this).

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Posted · Converting 3d ultrasound images to stl/obj

Bonjour Iassoan,

 

O.K. I'll try to put an NRRD export in there...  But, I may need some help testing it. 

 

This may sound strange, but as far as possible I try not to look at what other software are doing and how their interface work.  That way I am not influence when I design my own interfaces, and I solve the different interaction the way I think is the easiest for the user.  Of course most user interfaces are just basic good sense, so I guess there's not that many differences, but still I prefer to do things my way.  I've been doing this for the past 30 years and I'm still in business, so I may not be completely wrong...  

 

This mean that I do not have 3D slicer, or any such software, on my system (I actually never even look at 3D slicer's web pages until a few days ago).  So I have no way of testing if my NRRD files correct.  Would it be possible to send you a few files to make sure I got it right?

 

Yves

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Posted · Converting 3d ultrasound images to stl/obj

I would be happy to help you with verifying that the exported files are valid. If you want to try it yourself, it should be quite easy: drag-and-drop the nrrd file on 3D Slicer application window and click OK to load it. If loading is successful, you'll see three orthogonal views in the slice viewers. 

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Posted · Converting 3d ultrasound images to stl/obj

Hi everyone, I know is an old post but I think is a good idea keeping it updated for the people looking for a way to convert those files and print them.

 

In my case I have several mvl files and the only app I found which is able to open them with a really high quality was Baby sliceO from Tomovision. @Y_Martel you did an excellent app. It's intuitive and easy to use. I think I tried all the medical apps on earth until I found your one.

 

Unfortunately for me and my purposes it's quite expensive and there's no other option apart from Sonoview (To be honest I don't know if this app can export files in other formats or is just a simple Viewer).

 

I really appreciate if anyone knows more apps in order to open those medison files.

 

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