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sct-pipeline / ukbiobank-spinalcord-csa

Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.
MIT License
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Add subjects to exclude #60

Closed sandrinebedard closed 3 years ago

sandrinebedard commented 3 years ago

Description

This PR adds subjects to exclude in exclude.yml. The main causes for exclusion are that the FOV doesn't cover C2-C3 and poor data quality. I observed the following artefact multiple times: (sub-1132718_T1w.nii.gz) image image

I am not sure what could be the cause here.

jcohenadad commented 3 years ago

hum... could be aliasing of fat signal and/or motion. But i'm not sure i would necessarily remove it, as long as the output segmentation is correct: we do "see" the spinal cord between c2-c3, no?

sandrinebedard commented 3 years ago

But i'm not sure i would necessarily remove it, as long as the output segmentation is correct: we do "see" the spinal cord between c2-c3, no?

Yes, I agree for that image, but it maybe was not the best example 😬, my bad, I agree we can keep it. Some others also have motion artefact in addition. I'll check again with the segmentations for these images!

I find it ambiguous to know if we have enough slices to compute cord CSA: e.g: image

jcohenadad commented 3 years ago

in the case showed in https://github.com/sct-pipeline/ukbiobank-spinalcord-csa/pull/60#issuecomment-818246380, i would say there are not enough slices

sandrinebedard commented 3 years ago

@jcohenadad I removed the images from the list according your remark in https://github.com/sct-pipeline/ukbiobank-spinalcord-csa/pull/60#issuecomment-818228788 and kept the images that we would not have enough slices with the segmentation for cord CSA, everything should be ok now