Loading of GE/Kretz ultrasound volumes (.vol file)

shaeshaenee · August 13, 2019, 10:23pm

Continuing the discussion from Loading of GE/Kretz ultrasound volumes (.vol file):

HI,
i have a problem
-i tried importing sample data(s) shared in this discussion,
-i was able to load DICOME samples.
-i am not able to import 4DUltrasound sample, (even after re-saving as 3d Cart volume using 4dviewv.10) … it doesn’t load in slicer …actually it doesn’t load any data! there’s an ERROR in 3dsclier (“vtkSlicerKretzFileReaderLogic::LoadKretzFile failed: file ‘F:/Radiology sample data/Ultrasound/4D Ultrasound/IMG_20180620_2_1_cart.vol’ phi angle array is invalid (expected 260 elements, found 0”)
-the same goes for 3d ultrasound data sample , even after re-saving as non compressed using 4dview v.10)

i am using 3dslicer 4.8.0 and slicerhear is installed.
what am i doing wrong?
thanks in advance

lassoan · August 15, 2019, 3:13pm

Slicer-4.8 only supported spherical volumes. As far as I remember, current Slicer version supports rectilinear volumes, too.

Slicer-4.8 is more than 2 years old. Slicer is constantly being improved with new features and fixes, so if you use such ancient version then you miss out on many things. Always use at least the latest stable release.

lassoan · January 30, 2020, 8:02pm

2 posts were merged into an existing topic: Adding body to a Fetus

samsonaie · April 11, 2020, 4:24pm

Hi Andras,

Thanks a lot for your sharing. I had learned a lot from you post.
As you had mentioned in many post that GE may have private fileds in their DICOM ( dcm file ) , indeed!, I had followed your instruction to upload to GE’s 4D view v 10.5 ( per link in your Gitbub post ) , I successfully convert it to 3D Cart , and also set wavelet-compression to " none"
see the link below:

however I still fail to upload to Slicer v4.10 in which I had already included SlicerHeart extension
would you check the file for me and let me know if I had done anything wrong ?

the original dcm is in here:

thank you very much, it will certainly be great if you can guide me on how to load it to slicer successfully.

lassoan · April 26, 2020, 1:04am

I remember answering this question somewhere (maybe in another topic or forum) but cannot find it. Anyway, I could load both images without any problems by installing latest Slicer Preview Release (4.11, rev 29009) and SlicerHeart extension, then importing and loading them in DICOM module.

samsonaie · April 30, 2020, 3:18am

Yes, you had helped me. with the latest verison 4.11.-4-19 works fine.
Thanks again.

Guangxu_Li · May 31, 2020, 3:53pm

A very good ITK based example: https://github.com/plooney/kretz.
If you use 4D images, the ‘number of frames’ could be obtained in tag (0xd400, 0x0001).

lassoan · October 10, 2020, 2:28am

A post was split to a new topic: Segmenting GE Voluson ultrasound image

lassoan · December 23, 2020, 2:57pm

2 posts were split to a new topic: How to import ultrasound images from Samsung accuvix

Gregory_Van · December 23, 2020, 7:12pm

Hi,

Thank you Andras for putting all the work into this! Exactly what I was looking for! One question, is the github link for GE’s API files ( https://github.com/GEUltrasound/GE_CVUS_Loader/releases/ ) still in working order? I get a 404 error message but is that due to the fact that GE hasnt accepted me into the Edison Developer Program yet? I havent heard back from GE and just getting a little anxious.

Mich · January 17, 2021, 6:43pm

Hello! I have the Cartesian Vol format of a Voluson S8, How can I import it to the 3D Slicer ?because I have not achieved it, I hope you can help me.

lassoan · January 17, 2021, 6:49pm

Most probably you can use Image3dAPI to load that file. See detailed information here: GitHub - SlicerHeart/SlicerHeart: 3D Slicer extension for cardiac analysis.

If you share an example file then I can verify that SlicerHeart can indeed load it.

Mich · January 17, 2021, 7:01pm

Hello, thanks for the answer, I already downloaded the SliceHeart and I still can’t, I share the file for you to verify it, is it necessary to register in the Edison program to be able to achieve it?
https://www.dropbox.com/sh/63ujg7yl1o0pwcq/AADAcYlHdDpFb91CSbYbfnK5a?dl=0

lassoan · January 17, 2021, 7:38pm

These images can be loaded without Image3dAPI (without joining GE’s developer program), just using SlicerHeart.

After you installed SlicerHeart extension and restarted the application, drag-and-drop the .vol files to the application window and click OK to load them.

After median filtering and adjusting volume rendering transfer functions:

Mich · January 17, 2021, 10:41pm

Thanks! It´s beutiful

Coloradoultrasound · January 18, 2021, 6:02am

Of course; https://youtu.be/UHq0uyDvhaA

simongeek · January 20, 2021, 7:57am

Hi @lassoan,
I added the above file into my Slicer 3D, but volume rendering doesn’t work. Do you know what happened?

lassoan · January 20, 2021, 4:54pm

The volume rendering module documentation should help. Drag-and-drop of volumes from the data tree into views requires recent Slicer Preview Release.

simongeek · January 20, 2021, 5:24pm

Thanks @lassoan! It works!

Now, I would like to convert .vol files into .STL, it’s possible using Slicer 3D? Then, I am going to do segmentation on mesh data.

lassoan · January 20, 2021, 6:37pm

For 3D printing, you need to segment the image. See video tutorial here: https://youtu.be/UHq0uyDvhaA

In addition to the segmentation tools shown in the video, in recent Slicer Preview Releases you can also do local smoothing using a smoothing brush.

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Loading of GE/Kretz ultrasound volumes (.vol file)

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