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New loader integration: update datasets #13

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merged 7 commits into from
Mar 22, 2021

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mariehbourget
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@mariehbourget mariehbourget commented Mar 16, 2021

Related to #5.

This PR aims to update MRI anat and microscopy_png datasets following the integration of the new loader in ivadomed.
It also includes a small ct-scan dataset to test the file indexing from the decathlon spleen dataset used under CC-BY-SA 4.0 license.

@mariehbourget mariehbourget marked this pull request as draft March 16, 2021 14:45
@mariehbourget mariehbourget marked this pull request as ready for review March 22, 2021 16:57
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This PR is ready for review, it adds new file to test the new loader and ct-scan.
After the merge, I will create a new release to update the download link for data-testing in ivadomed PR 725.

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@andreanne-lemay andreanne-lemay left a comment

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LGTM! My only comment/concern is that I am wondering if only one subject will be enough for testing. It depends on the tests we plan to add, but with a single subject we can't do a training (we need at least 1 subject for training and 1 for validation). If that's not a test you planned to add, you can ignore this comment!

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LGTM! My only comment/concern is that I am wondering if only one subject will be enough for testing. It depends on the tests we plan to add, but with a single subject we can't do a training (we need at least 1 subject for training and 1 for validation). If that's not a test you planned to add, you can ignore this comment!

Thanks @andreanne-lemay for the review. I only want to test the force_index in the BidsDataframe. For training, we can test with MRI because they are nifti files as well.

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2 participants