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ivadomed / model_seg_ms_mp2rage

Model repository for MS lesion segmentation on MP2RAGE data from University of Basel
MIT License
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Fixed target suffix in config files for loading correct derivatives #47

Closed uzaymacar closed 1 year ago

uzaymacar commented 2 years ago

This PR resolves #41 by adding .nii.gz extension to all target suffixes across the four config files in order to load the correct derivatives. As discussed in ivadomed/ivadomed#1055, there was previously a bug in the loading of derivatives in this project due to the use of contains() during the loading process implemented in ivadomed/loader/bids_dataframe.py.

The fixed target suffix for lesion segmentation in this PR implements the randomly picking one of the two raters in each iteration strategy as before. This is because, as per the results presented in #40 through the benchmark.md file, this strategy achieves good Dice scores on both raters when compared to the other strategies.

However, if we implement the first option I presented here to take care of ivadomed/ivadomed#1055, then we might safely revert this PR as there will be no need for .nii.gz extension due to the enforcing of an exact match. (Further discussion with the ivadomed team is required to reach a decision, which will affect this PR.)

jcohenadad commented 1 year ago

Closing because another suffix is now used