Problem when opening a big TIF file about itkelastix HOT 8 OPEN

Dear Niels,

Thank you for taking the time.
I will report this to ITK.

Best regards,

Jérémie

from itkelastix.

Hi @Jeremie-BIC

Thank you for reporting this issue. Marius Staring (@mstaring) and I just looked at it, and it seems to us that it isn't a specific elastix/ITKElastix issue, but rather an ITK issue, or an itkwidgets issue. In that case, maybe you'd better report this to ITK (https://discourse.itk.org or https://github.com/InsightSoftwareConsortium/ITK/issues) or itkwidgets: https://github.com/InsightSoftwareConsortium/itkwidgets

Kind regards, Niels

from itkelastix.

This is most likely a limitation of the graphics subsystem (GPU does not have enough memory to fit the entire image in it) or VTK, the visualization library https://github.com/InsightSoftwareConsortium/itkwidgets uses. @floryst or @thewtex might have a better idea of where the problem comes from.

from itkelastix.

For itkwidgets, browser tabs usually have a ceiling on the memory allocation, though that usually results in a browser tab crash and not a blank image. If it's a TIF image, my guess would be that the underlying itk-wasm WebWorker is failing or crashing silently (possibly due to out-of-memory), leading to the display of a blank image...

from itkelastix.

Hi,

Thank you for help!

I understand that such a big file might be impossible to display in the Jupyter Notebook through the Itk Widget viewer.

However when I try to do a simpler operation, such as change the pixel spacing, I get an error. I think that the problem is happening when I open my image (using itk.imread).

I guess that, like Niels suggested, it is an ITK problem...

In case, I am putting the error I get. Any suggestion would be super appreciated.
Error is:

TypeError Traceback (most recent call last)
in
1 fixed_image.SetSpacing((25,25,25))
2 moving_image.SetSpacing((25,25,25))
----> 3 upscale_image.SetSpacing((2,2,4))
4
5 #fixed_image_resolution=fixed_image.GetSpacing() #prints spacing

TypeError: Expecting an itkVectorD2, an int, a float, a sequence of int or a sequence of float.
Additional information:
Wrong number or type of arguments for overloaded function 'itkImageBase2_SetSpacing'.
Possible C/C++ prototypes are:
itkImageBase2::SetSpacing(itkVectorD2 const &)
itkImageBase2::SetSpacing(double const *)
itkImageBase2::SetSpacing(float const *)

Thank you very much.

Best,

Jérémie

from itkelastix.

You might need something like:

spacing = itk.spacing((2,2,4))  # like this?
spacing = itk.spacing([2,2,4])  # or maybe like this?
upscale_image.SetSpacing(spacing)

from itkelastix.

Large scale registration support coming via https://github.com/InsightSoftwareConsortium/itk-dreg.

from itkelastix.

itk-widgets has support for large-scale images via NGFF. See: https://github.com/InsightSoftwareConsortium/itkwidgets/blob/main/examples/integrations/zarr/OME-NGFF-Brainstem-MRI.ipynb

from itkelastix.