Generate volume from non parallel frames.

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1

Hi
I’m using an endocavity linear ultrasound. The patient is scanned by rotating the probe on its own axe. So the série is a set of a non parallel frames.
I get from the device (mindray z60) only one file per series containing the all frames of the sequence.
On 3dslicer, I get a volume with parallel frames in the three axes.
Question how can I retransform to get the correct volume ( a rectangular frames rotating around the edge of the frames)
Thanks

2

Welcome to the Slicer community @derradji !
The good news is that there are two modules in Slicer that can do this:

  • SlicerIGT extension’s Volume Reconstruction module can reconstruct a volume from arbitrarily oriented slices.
  • SlicerHeart extension’s KretzFileReader module can reconstruct a volume from a rotational sweep.

Volume reconstructor module is probably simpler to make work on your data, as all you need is to have the image slices in a sequence node, with each slice pose correctly set from the DICOM file. This can be achieved by updating the DicomUltrasoundPlugin Python script to recognize your DICOM volume. As a quick test, you can convert the inage stack and add orientation information using this Python script.

KretzFileReader module contains both the DICOM reader and rotational volume reconstructor in one module and it is implemented in C++, so it is a bit more difficult to adapt to your data. However, since it is specifically developed to reconstruct rotational sweeps, it can create output volumes without holes at higher resolution.

If you provide an anonymized image then I can help with the implementation.

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Hi there
Sorry for my poor English.
Sorry for my latency. I’m using 3dslicer 4.8.1 because I’m using an aged computer.
I will soon update it.
Thank you for your response. After some tries. I was able to re export the volume in a new série as multiple parallel frames.
That is not what I want really.
Thé probe when rotating around it’s axis is creating a series of frames (I get one file with extension *.Dcm containing the all frames). On 3d slicer I get always a cube or parraleleped volume and not a cylindric volume.
I don’t know if I’m explaining right my idea.
I need to transform the file dcm into a new one correctly reformatted to get in final a cylindric volume.

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The image frames are loaded as a stack that appear as a rectangular block if you render them as a volume. You’ll get the cylindrical volume when you follow the steps I described in my answer above.