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Update argparse descriptions to make it clear that the script can also be used to compute MCC #4331

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merged 9 commits into from Jan 11, 2024

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@valosekj valosekj commented Jan 10, 2024

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Description

The sct_compute_compression function is meant to compute maximum spinal cord compression (MSCC) using the SC segmentation.
This PR updates the sct_compute_compression description to make clear that the function can also be used for maximum canal compromise (MCC) computation if spinal canal (aka CSF) segmentation is provided.
More context in #4330.

Currently, I have updated only the description (without changing any code). This assumes that users will read the description and will not provide spinal canal segmentation in combination with the -normalize-hc flag (normative database does not contain measures of the spinal canal). I made this clear by the following note:

'-normalize-hc',
metavar=Metavar.int,
type=int,
choices=[0, 1],
help='Set to 1 to normalize the metrics using a database of healthy controls. Set to 0 to not normalize. '
'\nNote: This flag is valid only if the spinal cord segmentation is provided by the flag "-i".',

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Resolves #4330

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Assuming the functionality works as intended, then I think the argparse changes are good!!

spinalcordtoolbox/scripts/sct_compute_compression.py Outdated Show resolved Hide resolved
spinalcordtoolbox/scripts/sct_compute_compression.py Outdated Show resolved Hide resolved
@joshuacwnewton joshuacwnewton added the documentation category: readthedocs, sourceforge, or SCT courses label Jan 10, 2024
@joshuacwnewton joshuacwnewton changed the title Add MCC to sct_compute_compression Update argparse descriptions to make it clear that the script can also be used to compute MCC Jan 10, 2024
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((I just tweaked the title of the PR to make it clear that no new functionality is actually being added.))

@joshuacwnewton joshuacwnewton added this to the 6.2 milestone Jan 10, 2024
@mguaypaq mguaypaq merged commit 3c0ff7e into master Jan 11, 2024
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@mguaypaq mguaypaq deleted the jv/4330_add_MCC_to_sct_compute_compression branch January 11, 2024 18:50
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Extend sct_compute_compression to MCC
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