Load files locally and align to volume from Stealth

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Jul 25, 2019, 12:12

Related to #15, but we also want to load:

• T1
• T2
• colour map

from files. These files are all registered together (they are aligned with each other), but not with the volume that lives on the Stealth.

@JonathanShapey's registration script creates a file called reg_T1stealth-2-b700.txt, which contains a transform. We must:

• load the data from that file and create a transform in Slicer, e.g. StealthToUpsampled
• place the above data (T1, T2, colour map) under that transform

After that, all volumes should be aligned.

Note to check: If the volume from the Stealth is transformed (e.g. under ReferenceToRas), then we should also apply that as a parent of StealthToUnsampled.

(In short: the Stealth volume and StealthToUnsampled should be at the same level, and the volumes loaded from local files should be children of StealthToUnsampled)

[tdowrick]

In GitLab by @RolandGuichard on Aug 12, 2019, 10:02

Since I am working a bit on this, the plan is to:

• Move the current Visualise button under the Live Reconstruction box. So far, this button is intended to be pressed after the live reconstruction is finished. However, this button does two actions: 1/ project the live reconstruction in the slice views (background) but also 2/ set the CT as foreground. Since we need now to toggle between different foregrounds, I will:
• Add a new Choose Image box that allow the user to toggle between loaded images (T1, T2 and CT as radio buttons) to set them as foregrounds in the slice views (from the above functionality) using radio buttons as selection and a Toggle push button.
• Apply the loaded colormap to the selected foreground if desired.

[tdowrick]

In GitLab by @RolandGuichard on Aug 13, 2019, 13:31

The issue is with point 3 above that the colormap is loaded as a volume and the label layer doesn't accept volumes.