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[BUG] Fix marching cubes not in the right space when CT is not aligned #25
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@larsoner would you happen to know why these tests are failing again? It might be
the PyQt version mismatch here but that's odd that it worked for a bit and then stopped working... I'll try with PyQt6 != 6.6.1 |
Ok, this should handle when images are not LIA now by going through scanner RAS. I also added some very standard boilerplate to the webpage since it was looking very lonely. If there's any issue with that I can split it out. Otherwise, looks good to go. |
Well there was actually a larger issue where all the tests were skipped because they didn't have |
Okay to merge by me |
Oh man well I looked again and the 3D rendering of electrodes when the CT is not aligned were off so then I had to think about with no recon-all what space the 3D rendering should be in. On
This way everything internally is in |
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This way everything internally is in scanner RAS and I think it just simplifies a lot all these transforms which caused this bug.
Agreed sometimes surface RAS is a pain, and scanner RAS is what nibabel
uses everywhere so if it makes stuff easier to work in scanner RAS it's a reasonable choice!
Feel free to merge if you're happy, just one comment about 1.6
Ok, thanks for the review, the last commit just finishes moving the 3D surfaces to scanner RAS, good that you approve of doing that. Sounds good, I'll wait a day or so in case I hear back from the people who reported the bug if they have a chance to test this before merging. Re 1.6, it's odd that it fails on |
All the examples look the same: https://output.circle-artifacts.com/output/job/aea15c4c-5071-434b-832d-f56b4ea42749/artifacts/0/dev/auto_examples/index.html The diff is a bit large to review but will merge tomorrow unless I come upon any other issues merging this into the other two WIP PRs. |
Fixes issue related to https://mne.discourse.group/t/wrong-ct-and-t1-alignment-shown-in-gui/7325/2