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Update MAP with latest Auto SVRTK reconstruction pipeline #10

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tomaroberts opened this issue Aug 21, 2023 · 0 comments · May be fixed by #13

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tomaroberts commented Aug 21, 2023 •

edited

Reconstruction script: https://github.com/SVRTK/auto-svrtk-scripts/blob/main/auto-brain-reconstruction.sh
- Input arguments: [full_path_to_folder_with_input_stacks] [full_path_to_the_outputs] 1 2.5 0.8 1
Model weights: https://gin.g-node.org/SVRTK/fetal_mri_network_weights/src/master

Basically need to:

update Dockerfile to pull newest weights
Alter SVRTK operator to use new .bash script
Check file pathing the same – nb: final file is called reo-SVR-output-brain.nii.gz, which is probably easiest to rename SVR-output.nii.gz for purposes of MAP.

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Updates aide-svrtk MAP with MONAI-based CNN #13

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