Add Volume Reslice to Slicelet #33

Closed tdowrick closed 3 years ago

In GitLab by @JonathanShapey on Dec 14, 2018, 16:46

Need to add Volume Reslice Driver from Slicer IGT

In GitLab by @DavidPerez-Suarez on Jan 14, 2019, 11:03

changed title from {-Update-} Slicelet to {+Add Volume Reslice to +} Slicelet

In GitLab by @ThomasDowrick on Mar 1, 2019, 16:14

Once the transform hierarchy has been setup, these are the settings in the Reslice Driver that will show the correct US slice in the 3D view

In GitLab by @ThomasDowrick on Mar 1, 2019, 16:18

Also need to enable 'Toggle Slice Visibility in 3D'. This is the button that does it in the Slicer GUI - will have to find the relevant function call to enable this programatically.

In GitLab by @AnastasisGeorgoulas on Mar 1, 2019, 17:41

This can be done programmatically with the SetSliceVisible method of vtkMRMLSliceNode. Example (assuming we want to make the first slice viewer visible in the 3D viewer):

slice_nodes = list(slicer.mrmlScene.GetNodesByClass("vtkMRMLSliceNode"))
slice_nodes[0].SetSliceVisible(1)  // or True

In GitLab by @AnastasisGeorgoulas on Mar 11, 2019, 16:55

@ThomasDowrick After your experiments last week, it seems it's better to render the image as a volume directly, without going through the slice view? If it is, do we still need the volume reslice driver?

In GitLab by @ThomasDowrick on Mar 11, 2019, 17:25

We'll still need to be able to use the Reslice Driver, to give the correct projections of the CT & Reconstructed US in the 3 Slice views when we move the probe.

We'll probably also need to show the Slice view in the 3D view, as it is only possible to show one 3D volume at a time (unless we use some of the experimental modules), and we will definitely want to show the 3D CT.

In GitLab by @AnastasisGeorgoulas on Mar 11, 2019, 17:46

My understanding was that the slice views would be specific projections (e.g. axial, coronal, saggital), and wouldn't move around with the probe. Maybe @JonathanShapey can clarify.

Since the slice views could be occupied by something else, maybe we should also look into how else we can display the US in the 3D view (working around the one volume restriction - maybe using segmentations?)

In GitLab by @ThomasDowrick on Mar 11, 2019, 20:12

They will be used show the axial/coronal/saggital planes, but each plane is made up of multiple slices of the CT/3D ultrasound data. The exact slice that will be shown will correspond to the location of the probe.

In GitLab by @JonathanShapey on Mar 11, 2019, 22:15

Thanks @ThomasDowrick that's very nicely put.

In GitLab by @AnastasisGeorgoulas on Mar 11, 2019, 22:22

Thanks for clarifying - previous discussions had given the impression that the slice views would be static, and that the particular slice displayed would be chosen by the sliders, not follow the probe location.

In GitLab by @JonathanShapey on Mar 11, 2019, 22:33

@AnastasisGeorgoulas Sorry for causing any confusion... when you freeze the point of the probe you should then be able to scroll through the views in each plane individually but when it's "live" they change as per the probe tip (see @ThomasDowrick 's explanation). This is how most navigation system's operate so I can show you on the Stealth machine when we're next in the lab together.

In GitLab by @AnastasisGeorgoulas on Mar 14, 2019, 18:55

If we don't want to include the whole Volume Reslicer Driver widget as an extra tab, the functionality should be accessible programmatically as:

logic = slicer.modules.volumereslicedriver.logic()
logic.SetModeForSlice(logic.MODE_INPLANE, slice_nodes[0])

In GitLab by @AnastasisGeorgoulas on Mar 19, 2019, 11:42

Notes from @ThomasDowrick (please correct if wrong!):

To show live US image in 3D viewer correctly:

Show the 2D image in a slice viewer
Volume Reslice Driver: set mode for slice viewer to Inplane (or another option) to show slice in its real orientation
Can then make that visible in the 3D viewer

To have slices track the probe location:

Set up transform hierachy
In Volume Reslice Driver, choose appropriate transform under “Driver”

In GitLab by @ThomasDowrick on Mar 19, 2019, 11:54

Yes, that's correct.

We spoke in the meeting yesterday about whether we need to show the live US data from the BK in the 3D view, in short, we don't, but we will probably want to display something indicative of the area being imaged, such as a coloured triangle.

I would add a few things for the second part:

Set the mode in the reslice driver to Axial, Sagittal and Coronol for RYG slices.
Set the RYG views to display the reconsturcted US volume (assume the node will be called 'liveReconstruction')

In GitLab by @ThomasDowrick on Mar 21, 2019, 10:27

The US image comes into Slicer upside down, so we probably need to flip this using the reslice driver 'advanced' options. Can confirm if this is required after testing today.

In GitLab by @JonathanShapey on Apr 8, 2019, 09:04

assigned to @RolandGuichard and unassigned @DavidPerez-Suarez