Spacingd cause kernel crashing

[emi-dm]

Certainly! Here's a draft for your GitHub issue:

---

Issue Title: Bug in Monai Spacingd Transformation

Description:
I encountered an issue with the Monai library related to the Spacingd transformation. However, I'm unsure if it's due to an error on my part. I've also provided a notebook to reproduce the issue.

Steps to Reproduce:
You can reproduce it in the notebook: https://colab.research.google.com/drive/1ahj3IQqetxRxeVQm0tNpdqXJOq9nTxRT?usp=sharing

Expected Behavior:
The Spacingd transformation should correctly handle spacing adjustments without causing any unexpected artifacts.

Thanks in advanced!

[KumoLiu]

Hi @emi-dm, I ran the notebook you shared, and found the problem is from the Orientationd.
After your Orientation, the affine will be wrong.

In MONAI, we assume the affine matrix is LPS in ITKReader which should be your default reader.

MONAI/monai/data/image_reader.py

Line 176 in ff43028

affine_lps_to_ras: whether to convert the affine matrix from "LPS" to "RAS". Defaults to ``True``.

Hope it helps, thanks.

MONAI/monai/data/image_reader.py

Line 282 in ff43028

header[MetaKeys.SPACE] = SpaceKeys.RAS if self.affine_lps_to_ras else SpaceKeys.LPS

[KumoLiu]

I saw you modified the notebook and removed the Orientationd, is there still an issue exists?

[emi-dm]

Yes, I would like to use Spacingd and Orientationd transformations to standardize my images. These have a base resolution of 512x512 px, I would like to normalize all volumes to the same spacing and finally have a common resolution (e.g. 256x256 px).

I restored the original version of the notebook.

Thanks in advanced!!

[KumoLiu]

Hi @emi-dm, I tried with larger pixdim, and then the kernel will not crash. So the problem should be the limited RAM resource.
monai.transforms.Spacingd(keys=["image"], pixdim=[1.0, 1.0, 1.])

Thanks.

[emi-dm]

Thank you very much, it is true that by decreasing the spacing space I am generating more information, hence I run out of RAM.

Thanks for all the information and for giving me a hand!

[emi-dm]

@KumoLiu , Do you know of any resources where I can learn more about this?