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sct-pipeline / csa-atrophy

Evaluate the sensitivity of atrophy detection with SCT
https://csa-atrophy.readthedocs.io/
MIT License
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Error: resampling of disk labels fails #74

Closed PaulBautin closed 4 years ago

PaulBautin commented 4 years ago

In last results certain subjects (notably sub-brnoUhb*) have disk-labels with non-int values. Example: sub-brnoUhb02_T2w_labels-disc-manual_RPI_r.zip The function sct_resample uses by default a linear resampling that is not adequate for these labels. A solution is to use an interpolation to nn (nearest neighbour). However, labels seem to be missing on output images.

test: command: sct_resample -i sub-brnoUhb02_T2w_labels-disc-manual.nii.gz -mm 0.8x0.8x0.8 -x nn -o test.nii.gz file: sub-brnoUhb02_T2w_labels-disc-manual.zip result image: test.zip

jcohenadad commented 4 years ago

this behaviour was expected, see https://github.com/sct-pipeline/csa-atrophy/issues/59#issuecomment-683036793

one workaround is to dilate the labels, (eg sct_math -dilate 3) and then resample with NN.