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Practicals 1-4 #24

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@clead6 clead6 commented Nov 21, 2024

  • Finished writing up practicals 1-4
  • Updated the setup instructions and added a link to download dataset and jupyter notebooks.

@clead6 clead6 requested a review from davecash75 November 21, 2024 15:13
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github-actions bot commented Nov 21, 2024

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

  • 🎯 correct output
  • 🖼️ correct figures
  • ❓ new warnings
  • ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/compare/md-outputs..md-outputs-PR-24

The following changes were observed in the rendered markdown documents:

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 index.md                                           |   3 +-
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 md5sum.txt                                         |  26 +-
 practical1.md (new)                                | 617 ++++++++++++++
 practical2.md (new)                                | 232 +++++
 practical3.md (new)                                | 116 +++
 practical4.md (new)                                | 196 +++++
 setup.md                                           | 262 +++---
 99 files changed, 1276 insertions(+), 1591 deletions(-)
What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2025-01-06 14:33:39 +0000

github-actions bot pushed a commit that referenced this pull request Nov 21, 2024
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Hi @clead6 apologies for delay in reviewing, but this is great, very much appreciate all the changes and work you have added to these practicals and the notebooks. All of the notebooks ran for me using the new environment YAML file you provided. Most of my suggestions are minor formatting things.

For all practicals, I think it would be good to put a
::::::::::::::::::::keypoints
::::::::::::::::::::
section at the end with the 2-3 main takeaways from each practical.
Over to you @jamie-mcclelland - apologies again it took me so long.

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jamie-mcclelland and others added 6 commits December 13, 2024 09:57
added instructions to install itk-snap and also specify version used for practical (note - still need to add specific version used)
minor edit to practical 1 instructions
modified sections 2.1 and 2.2
also minor edits to make formatting consistent
updated section 2.3 (prev 2.4)

also modified figures to display as desired
updated figures for opening image
some updates to 2.4
github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
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clead6 commented Dec 16, 2024

Related to an above comment about the setup instructions. Do we want to explain:

  • how to open the created environment in VSCode?
  • how to open the correct folder in VSCode? and the jupyter notebooks? they do need to download the correct extensions.

github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
@clead6
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clead6 commented Dec 16, 2024

Related to an above comment about the setup instructions. Do we want to explain:

  • how to open the created environment in VSCode?
  • how to open the correct folder in VSCode? and the jupyter notebooks? they do need to download the correct extensions.

Added this in commit 4aa1227

github-actions bot pushed a commit that referenced this pull request Dec 16, 2024
finished section on loading multiple images (2.4)
made other minor changes to previous sections
updated itk-snap install instructions
updated section on image layer inspector (now numbered 2.4)
modified section 3 - converting dicom image to nifti - now use itk-snap instead of simpleitk
changes to section numbers and some formatting
github-actions bot pushed a commit that referenced this pull request Jan 6, 2025
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3 participants