Experiment: Inference of a 3d nnUNet on a single slice

[rohanbanerjee]

During a discussion with @kennethaweberii and @MerveKaptan, we discussed if our 3d automatic segmentation model would work if it has to segment the spinal cord on a single slice.

I am currently investigating this and will update this issue with the different outcomes that I get.

[jcohenadad]

from ROHAN: Sct_image padding doesn’t work for a single slice. Throws the error “ERROR: you need to specify a 3D input file.”
--> TODO: open issue and crossref

[jcohenadad]

from ROHAN: I wrote a script to pad the images but the nnUNet still throws an error of not being able to segment the images. Investigating this now (Will update all of this on the issue).

[rohanbanerjee]

Sct_image padding doesn’t work for a single slice. Throws the error “ERROR: you need to specify a 3D input file.”
--> TODO: open issue and crossref

The issue related to this comment can be found here: spinalcordtoolbox/spinalcordtoolbox#4223 (comment)

I wrote a script to pad the images but the nnUNet still throws an error of not being able to segment the images. Investigating this now (Will update all of this on the issue).

The issue related to this comment can be found here: spinalcordtoolbox/spinalcordtoolbox#4222 (comment)