I have DICOM data containing 2D echocardiography time sequence. I want to visualize and orient these in the 3D viewer so that I can overlay them with 3D CT/MRI images from the same patient. What’s the best way to do this? I tried using the Echo Volume Render, but it didn’t seem to work, and I understand it’s designed for 3D or 4D echo data.
Most 2D data lacks the spatial geometry information needed to automatically display it relative to 3D data. You can manually transform the 2D echo data to align with the anatomy or maybe you can find some automatic way to do that, but it’s a hard problem.
You can use the Volume Reconstruction module in SlicerIGT extension to reconstruct a 3D volume from position-tracked ultrasound image slices. Do you know the position and orientation of each image slice?
In the screenshot it seems that you show a single slice of the image. If the image was acquired with a straight translational sweep then you can get a rough 3D reconstruction by loading the frames as a single 3D image (instead of a time sequence of 2D images) using the Advanced checkbox option in the DICOM module.
Hi Andras, thanks for the suggestion. I don’t know the position/orientation of each image slice, and I don’t think that information was recorded. As far as I know, the data was not acquired with a straight translational sweep either, just a stationary transducer
I think for now, all I want is a way to manually position, scale, and orient a slice view in the 3D viewer.
I came up with a working but clunky solution. I used the Interactive transform to translate and orient my 2D echo sequence, then used “Rotate to volume plane” on the red slice and showed it in the 3D view. With this, I can view the echo data together with 3D segmentation data from MRI.
Is there a better way to do this?
Also, I saw I can Scale the data using the Transform, but it looked like I can only scale it one direction at a time. Is there a way to do isotropic scaling?
That sounds like a workable approach.
For scaling, you should determine the scale of the US image in patient space and change the slice spacing accordingly (in the Volumes → Volume Infromation) so it should naturally match the MR space.
Thanks, that works well!
I wonder if the Fiducial Registration Wizard module would work in this situation. My understanding is that 2D is essentially just a single slice 3D volume.
Yes, it can be easier to align the slice to a volume placing 3 points on the image slice and then marking the same 3 points in the CT/MR.
If you want to use interactive transform handles then you can keep the slice view automatically aligned with the image slice by using the Volume Reslice Driver module (in SlicerIGT extension). Without that you would need to keep clicking “Rotate to volume plane” button to manually align the slice view.
Thanks both for the tips!