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Test the model with anatomical variations #75

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@yw7 yw7 commented Oct 9, 2024

!!!NOT TO BE MERGED NOW!!!

This PR is for testing the model against anatomical variations.

In this PR we used the C7T1 and T12L1 landmarks to determine abnormal number of vertebrae instead of using the normal number of vertebrae in each region as maximum.

We can test this using the dataset referenced in the following paper: https://doi.org/10.1038/s41597-021-01060-0
#74

11 Thoracic Vertebrae ✅ 4 Lumbar vertebrae✅ 6 Lumbar Vertebrae❌ 6 Lumbar Vertebrae✅
sub-verse636_ct_11t_sag_0 5_step2_output_tags sub-verse627_ct_4l_sag_0 5_step2_output_tags sub-verse623_ct_6l_sag_0 5_step2_output_tags sub-verse585_ct_6l_sag_0 5_step2_output_tags

Note: The current main branch is also support 4 and 6 lumbar vertebrae when full field of view is provided:

4 Lumbar vertebrae✅ 6 Lumbar Vertebrae✅
whole_amuPAM50016_T1w_sag_0 5_step2_output_tags sub-verse585_ct_6l_sag_0 5_step2_output_tags (1)

…variations

Expanded the dictionary to cover additional spine vertebrae labels from C8 through L9, enhancing the segmentation capabilities for a broader range of spinal regions. Updated `region_max_sizes` to accommodate these changes, allowing for more inclusive processing of vertebraes in the iterative labeling. Removed the constraint that limited processing to only the first two landmarks, addressing a prior limitation and improving overall accuracy in landmark-based segmentation. This work addresses part of the spine segmentation enhancements.
@yw7 yw7 changed the base branch from main to for-r20241005 October 9, 2024 15:07
@yw7 yw7 added the invalid This doesn't seem right label Oct 9, 2024
@yw7 yw7 deleted the branch main October 11, 2024 14:32
@yw7 yw7 closed this Oct 11, 2024
@yw7 yw7 reopened this Oct 11, 2024
Base automatically changed from for-r20241005 to main October 11, 2024 15:05
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