Visualisation options #80

Open tdowrick opened 3 years ago

In GitLab by @DavidPerez-Suarez on Aug 20, 2019, 16:58

List of images (and buttons) to be loaded

marked done what's on load-image-files

[ ] MRI T1 + C (needs update name)
[ ] MRI T2 (needs to be added)
[ ] diffusion MRI (AKA, colourmap) - difference of diffusion. (needs to update name)
[x] Tumour segmentation (green)
[x] Nerve Segmentation (yellow)
[x] CT

Visualisations defaults

screen for neurostimulation (2 x 2)
- background: t1 + c (with options to change between: t1, t2 or ct)
- overlaid: diffusion + oppacity change
- top: both segmentation + oppacity change (so neurostimulation points can be seen)
US (3 x 2, or 2 x 2)
- background: CT (options: T1, T2, CT)
- overlaid: diffusion (on/off)
- top: US reconstruction as grayscale

Note: The contrast and intensity of the diffusion don't look as nice as it should by default. Adjusting the intensity to min=0, max=0.5 and level=0.2 seems to bring the colours nice and clear.

Views

@JonathanShapey could you add to this issue the snapshots from the presentation you have with the data loaded for these two options and with the panels divided into the portions you would like (2x2, 3x2, etc...)?

In GitLab by @DavidPerez-Suarez on Aug 20, 2019, 17:10

changed the description

In GitLab by @JonathanShapey on Aug 21, 2019, 11:53

Fig5a

Fig5b

SBN_user_interfaceaDiffusion_MRI_data_of_a_patientSBN_P1__with_a_vestibular_schwannoma.

In GitLab by @JonathanShapey on Aug 21, 2019, 11:53

I'll do a 3 x 2 view for the ultrasound (b) and will upload this in due course

In GitLab by @AnastasisGeorgoulas on Aug 29, 2019, 17:22

mentioned in merge request !22

In GitLab by @MianAhmad on Aug 30, 2019, 14:30

mentioned in commit 3540d0d1d4c6d3b36236f8dab90dcd6bb4d36577

In GitLab by @AnastasisGeorgoulas on Oct 2, 2019, 19:42

The blending/composite mode can result in only seeing a subset of each image. To change the blending mode:

for slice in ['Red', 'Yellow', 'Green']:
    l = slicer.app.layoutManager().sliceWidget(slice).sliceLogic()
    l.GetSliceCompositeNode().SetCompositing(l.GetSliceCompositeNode().Add)

Options include Alpha, ReverseAlpha, Add and Subtract

We may also need to load the images as centred:

_, node = slicer.util.loadVolume(dialog.selectedFiles()[0],
                                             {"show": False, "center": True},
                                             returnNode=True)

UCL / SkullBaseNavigation