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sct_image: Clarify descriptions for -setorient commands #3938

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merged 3 commits into from
Nov 10, 2022

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Description

This PR is a direct response to the user confusion from https://forum.spinalcordmri.org/t/how-to-use-sct-image-to-fix-the-orientation-of-the-header-and-data-array-setorient-data-vs-setorient/848/1.

My main goals were to:

  • Clarify that -setorient modifies the header and array in tandem.
  • Clarify the usage of -setorient-data, since I had to explain its usage multiple times to the user.

Linked issues

Fixes #3741.

This is to clear up some confusion raised by a user on the forum,
since `-setorient` *doesn't* just modify the header.
This is to clear up some confusion raised by a user on the forum,
since `-setorient` *doesn't* just modify the header.
@joshuacwnewton joshuacwnewton added documentation category: readthedocs, sourceforge, or SCT courses sct_image context: labels Nov 9, 2022
@joshuacwnewton joshuacwnewton added this to the 5.8 milestone Nov 9, 2022
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@mguaypaq mguaypaq left a comment

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This is much clearer, thanks! These are particularly confusing options, so it's good to document them extra explicitly, as you're doing here.

@joshuacwnewton joshuacwnewton merged commit 7462120 into master Nov 10, 2022
@joshuacwnewton joshuacwnewton deleted the jn/3741-clarify-setorient-help-description branch November 10, 2022 17:45
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Help description for sct_image -setorient is misleading
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