Wrong Orientation/Origin for multichannel volumes (4D) using Slicer - Issue visualizing BRATS images on 3DSlicer

[SachidanandAlle]

BRATS and prostate, which have more than one modality. It seems we're having the same problem I had before. Once Slicer loaded the volume, I didn't find a way to get back all the modalities

This was something I left in the to-solve list. As workaround solution, I get the modalities before I loaded in Slicer

In addition to the multimodality issue in Slicer, the BRATS data seems to have a problem with the orientation

• From @diazandr3s

[fepegar]

This is because Slicer (which uses SimpleITK) cannot read these images and just chooses to assign some default orientation when images are 4D. A way to solve this is to first check the shape of the images (without Slicer) and use a custom loader if we know that Slicer will struggle reading the file.

[diazandr3s]

Another way to follow is showing ONLY one modality in Slicer, so the user provides points for DeepGrow, and visualizes the automatic label. However, for inference, we use all the available modalities.

[fepegar]

Even if you show the user only one modality, the image needs to be loaded correctly first. This might be relevant, although I think it's designed for images where time is 4th dimension: https://www.slicer.org/wiki/Documentation/Nightly/Modules/MultiVolumeExplorer

[SachidanandAlle]

Moving to backlog.. not a priority for 0.2 version release