Update batch_single_subject.sh and process_data.sh to match changes to 2024 SCT Course Slides
#25
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Rootlets and lesion analysis should be incorporated more deeply into the tutorials, but for this year's SCT Course, they are in the "New Features" section, so we should put them at the end as to not disrupt the flow of the script.
valosekj
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valosekj
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Nov 26, 2024
valosekj
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valosekj
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valosekj
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Co-authored-by: Jan Valosek <[email protected]>
Co-authored-by: Jan Valosek <[email protected]>
…oints No clue why they were changed, but better to match them than have a hair--pulling bug later
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`sct_deepseg` QC is not yet available in `sct_qc` script
Since the sections are moved to the end of the course, these are now redundant.
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batch_single_subject.sh to match changes to 2024 SCT Course Slidesbatch_single_subject.sh and process_data.sh to match changes to 2024 SCT Course Slides
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Showing users that they can specify an output folder is important!
Now they are more in line with the sections in the slides
This is the preferred syntax for the script, rather than using `\` to split the command over multiple lines.
To match the slides.
Now matches the slides
We don't have time to debug "RuntimeWarning: invalid value encountered in scalar divide" before SCT course.
This will improve debugging, so that we can see what step actually fails. Also, by splitting up the steps, we can continue to the next step on failure of an earlier step thanks to "if: always()".
`grep` returns 0 if found, and 1 if not found. But we want the opposite: 1 if warning/error is present, and 0 if there are no warnings/errors. So, we need to invert the output code. I have no idea why these checks lasted as long as they did without this `!` inversion. The `grep` commands only used options `-iF`, meaning (case-insensitive) and (non-regex strings), so the options don't have anything to do with it. Hopefully this will fix the erroneous failures?
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OK, I think this is ready to be merged. I did one more once-over and updated the commands to match the slides once again (there were some discrepancies in the "new features" section, along with some updates to various slides since our last meetings). I'm happy at any point this weekend to merge + remake the |
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all right let’s merge! thank you so much for your outstanding dedication @joshuacwnewton ! |
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In the course slides, this line has an additional (But it's on a "red" slide, so maybe this is intentional?) Same thing with this line (also on a "red" slide): The next (and last) command in this section does have the QC report: |
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Fixes spinalcordtoolbox/spinalcordtoolbox#4729.
Fixes spinalcordtoolbox/spinalcordtoolbox#4727.
Fixes #24.