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Update PAM50 with the spinal label files produced by the University of Calgary's Philips Lab #3952

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jcohenadad opened this issue Nov 21, 2022 · 3 comments · May be fixed by spinalcordtoolbox/PAM50#3
Open

Update PAM50 with the spinal label files produced by the University of Calgary's Philips Lab #3952

jcohenadad opened this issue Nov 21, 2022 · 3 comments · May be fixed by spinalcordtoolbox/PAM50#3
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@jcohenadad
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jcohenadad commented Nov 21, 2022 •
edited by joshuacwnewton
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A group in Calgary has improved the spinal labeling of the PAM50 template. An article is under review, but the label files are already available at https://github.com/PhillipsLab/pam50.

It would be nice to update our current spinal level files with the new ones.

A few considerations:

  • We would ideally integrate this change in a stable release before the article is published. Publication date is still unclear, but likely early 2023 (which would correspond to v5.9).
  • Our users using these labels need to be informed that they have changed, otherwise their analysis results will change without them knowing why.
  • Based on the previous point, should we release under v6.0 (because major cross-compatibility break). Note, however, that I don't think many people are using this spinal level. But I could be wrong...
@joshuacwnewton joshuacwnewton changed the title Update spinal labeling Update PAM50 with the spinal label files produced by the University of Calgary's Philips Lab Nov 24, 2022
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An article is under review

Is there an arxiv/preprint copy of the article, by chance? I'm curious how exactly the files were improved. 👀

@mguaypaq mguaypaq modified the milestone: 5.8 Dec 1, 2022
@joshuacwnewton joshuacwnewton added this to the 6.0 milestone Jan 13, 2023
@joshuacwnewton joshuacwnewton mentioned this issue Jan 14, 2023
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@joshuacwnewton
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Just to check... As per #1192, if we're updating the spinal level files, then we would also have to update the cord file too, no?

@jcohenadad
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Just to check... As per #1192, if we're updating the spinal level files, then we would also have to update the cord file too, no?

I don't think so, because the spinal level files are only single voxels, and are independent from the PAM_levels file (which is a 'colored' segmentations, hence does depend on the PAM50_cord). So, in this case, changing the spinal levels won't change PAM50_levels

@sandrinebedard sandrinebedard linked a pull request Feb 13, 2023 that will close this issue
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@joshuacwnewton joshuacwnewton removed this from the 6.0 milestone Jul 12, 2023
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