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Merged
wyli merged 20 commits into from
Sep 11, 2022
Merged

Update 3d-segmentation tutorials #916

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KumoLiu Jul 21, 2022
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KumoLiu Aug 6, 2022
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KumoLiu Aug 22, 2022
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easy-integrate-bundle-v1
KumoLiu Aug 22, 2022
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 22, 2022
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add multigpu implementation
KumoLiu Aug 23, 2022
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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KumoLiu Aug 23, 2022
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Merge branch 'main' of https://github.com/Project-MONAI/tutorials int…
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Merge branch 'main' of https://github.com/Project-MONAI/tutorials int…
KumoLiu Sep 9, 2022
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minor fix
KumoLiu Sep 9, 2022
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Merge branch 'main' into update_seg_tutorials
wyli Sep 11, 2022
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2 changes: 1 addition & 1 deletion 3d_segmentation/challenge_baseline/README.md
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Expand Up @@ -64,7 +64,7 @@ During training, the top three models will be selected based on the per-epoch va

The training uses convenient file loading modules and a few intensity and spatial random augmentations using [MONAI](https://github.com/Project-MONAI/MONAI):

- `LoadImaged`, `AddChanneld`, `Orientationd`, `Spacingd`, `ScaleIntensityRanged`
- `LoadImaged`, `Orientationd`, `Spacingd`, `ScaleIntensityRanged`

Load the image data into the LPS orientation (Left to right, Posterior to anterior, Superior to inferior), with a resolution of 1.25mm x 1.25mm x 5.00mm, and intensity between [-1000.0, 500.0] scaled to [0.0, 1.0].

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2 changes: 1 addition & 1 deletion 3d_segmentation/swin_unetr_brats21_segmentation_3d.ipynb
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Expand Up @@ -479,7 +479,7 @@
"torch.backends.cudnn.benchmark = True\n",
"dice_loss = DiceLoss(to_onehot_y=False, sigmoid=True)\n",
"post_sigmoid = Activations(sigmoid=True)\n",
"post_pred = AsDiscrete(argmax=False, logit_thresh=0.5)\n",
"post_pred = AsDiscrete(argmax=False, threshold=0.5)\n",
"dice_acc = DiceMetric(\n",
" include_background=True, reduction=MetricReduction.MEAN_BATCH, get_not_nans=True\n",
")\n",
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