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Custom strategy to determine the slice coordinate in the reference space #49

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jankrepl opened this issue Aug 17, 2021 · 0 comments
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@jankrepl
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jankrepl commented Aug 17, 2021

In #40 a very simple logic of determining the refspace coordinate was implemented (inside of download_dataset_parallel). Namely:

  1. Let the user choose detection_xy=(x, y) which is a fixed point in the image. Be default it is (0, 0).
  2. Query the Image-To-Reference API (xy_to_pir) to get the corresponding (p, i, r) (link)
  3. The slice coordinate is then just p if axis="coronal" or r if axis="sagittal".

The above is clearly not ideal. See below some other ideas

  1. Keep the current algorithm with a dynamic default - finding the middle of the image automatically since it may vary for each section image
  2. Query all 4 corners of the image using xy_to_pir and let the slice coordinate be their average
  3. Use the section_number provided by Allen (see What is the section number provided by Allen? Can we use it? #50) together with the slice ?thickness?
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