Segmentation process does not start in GUI

[kueckelj]

Hello, I am trying out the GUI from Raidionics. I want to segment a low grade glioma. For that I load a .nii.gz file as input, then click on Actions >> Preoperative Segmentation >> Low-Grade Glioma >> OK. The process does not start, hangs at 0% for a while and then the GUI returns to a state as if nothing happened.

What am I missing?

[dbouget]

Hi @kueckelj,

The GUI hanging at 0% should only happen the first time you run a model, while the model is being downloaded locally on your machine, but no prompt is showing on the right-hand side.

For running the low-grade glioma segmentation model, a FLAIR input MR scan is required (and is the only MR sequence type the model can work with). On the right-hand side panel, the sequence type should also properly indicate the actual type for the MR scan (you can use the drop-down widget to select from the 4 possible MR scan sequence types).

Generally, you can have a look at the log file (⌘ + L, or Settings > Logs) where it might be indicated the reason why the expected results were not produced. If there is an error message inside the log file, you can also upload it here so that I can have a look.

[kueckelj]

Thank you! I'll try and report!

[kueckelj]

Now I have a similar problem with postoperative segmentation of a GBM. While I have managed to create the preoperative tumor mask (first image), the postoperative segmentation of the postop-MRI fails, too. Progress 1/9 is the only step I see. Am I missing something again? I am using the T1-CE.nii.gz file.

[dbouget]

Yes, this is because the image you provided is still assigned as being a preop image (timestamp T0 on the right-hand side panel).
You have to press on the + icon (as indicated by the red arrow) to create a new timestamp (timestamp T1 will be assumed as containing postoperative data).

Running a postoperative task should then work, if the timestamp T1 is populated with the correct images.
In the upcoming stable release, this will be fixed so that if only postoperative data are provided as timestamp T0, the postoperative tasks will run on those.

[kueckelj]

Thanks. With "with the correct images" you mean both T1 and T1-CE sequences?

[dbouget]

You need at least a T1-CE sequence for the "contrast-enhancing" models to run, and at least a FLAIR sequence for the "non contrast-enhancing" models to run. Any additional sequence might be used, depending on what is available for each model, but is not a requirement.

[burkotOndrej]

The GUI hanging at 0% should only happen the first time you run a model, while the model is being downloaded locally on your machine, but no prompt is showing on the right-hand side.

I had a similar issue and your reply also helped me, thanks a lot. I thought that models are downloaded along with Raidionics installation file.