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effigies avatar effigies commented on June 3, 2024

Symlinks are resolved by the container kernel, not the host kernel. A relative path that doesn't go outside the mount would work as expected, but an absolute path to a location that does not exist in the container will just be a dangling symlink inside the container.

mkdir -p /tmp/datasetA/sub-123/anat/  mkdir -p /tmp/datasetBln -s /tmp/datasetA/sub-123 /tmp/datasetB/echo "This exists" > /tmp/datasetA/sub-123/anat/sub-123_T1w.nii.gzcat /tmp/datasetB/sub-123/anat/sub-123_T1w.nii.gz 
This existsdocker run --rm -it -v /tmp/datasetA:/data:ro busybox cat /data/sub-123/anat/sub-123_T1w.nii.gz
This existsdocker run --rm -it -v /tmp/datasetB:/data:ro busybox cat /data/sub-123/anat/sub-123_T1w.nii.gz
cat: can't open '/data/sub-123/anat/sub-123_T1w.nii.gz': No such file or directorydocker run --rm -it -v /tmp/datasetB:/data:ro busybox ls -lR /data                                
/data:
total 0
lrwxrwxrwx    1 1000     1000            21 Oct 23 19:44 sub-123 -> /tmp/datasetA/sub-123

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nx10 avatar nx10 commented on June 3, 2024

Oh wow I did not know that thanks!

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