When running sct_process_segmentation , the -vert option expects a vertebral level range (two values). If I want to restrict the analysis to a single level (e.g., C1), should I set -vert 1:1 ? Or should I use -vert 1:2 (since the C1–C2 interval contains C1 but excludes C2)?
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Hi @marcoganz,
Apologies for the confusion! The -vert argument can also accept single values (-vert 1) or multiple single values separated by commas (-vert 1,3,5). (Source)
The documentation is not clear about this (as you mention, it lists only the slice range syntax) so we will update this promptly.
Kindly,
Joshua
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Thanks Joshua.
-vert 1:2 would consist of two vertebral bodies the C1 + C2
-vert 1,2 would be the same as -vert 1:2, right?
-vert 2:3 would be C2+C3, thus partially overlapping with -vert 1:2 (C2 would be shared)
Yes, exactly!
(Under the hood, the input syntax is just converted into a list of numbers, e.g. [1,2], and [1,2], and [2,3] for your examples.)
One other important note: The -perlevel 1 flag will cause metrics to be outputted on a per-level basis (i.e. each vert level will have its own row in the output CSV).
So, for -vert 1:2, instead of averaging the metrics for 1+2, it will show the individual metrics for 1 and 2 separately.