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Merged
merged 5 commits into from
Jun 12, 2022

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wyli
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@wyli wyli commented Jun 5, 2022

Signed-off-by: Wenqi Li wenqil@nvidia.com

Fixes #130

  • basic binary seg example with random 2D samples + 2d unet for 3D inputs
  • inference with a sliceinferer

Screenshot 2022-06-05 at 22 07 12

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Ready

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  • Notebook runs automatically ./runner [-p <regex_pattern>]

@wyli wyli marked this pull request as ready for review June 5, 2022 22:15
@wyli wyli force-pushed the 2d-3d-training branch from f78a1e5 to 2b320e8 Compare June 5, 2022 23:05
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Hi @wyli ,

Thanks for the quick demo.
Could you please help add more description for the 2 typical methods in this example?
(1) Randomly crop slices for training, (2) Slices for inference.
Or maybe it's better to convert it into a jupyter notebook? So we can include the plot charts of matshow3d or image slices in it?

Thanks.

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wyli commented Jun 6, 2022

thanks, I'll try to convert this script into a notebook example.

wyli added 4 commits June 10, 2022 15:12
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the 2d-3d-training branch from b4648a5 to 1dfa20c Compare June 10, 2022 14:31
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Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli merged commit c3a7e95 into Project-MONAI:main Jun 12, 2022
@wyli wyli deleted the 2d-3d-training branch June 12, 2022 10:06
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wyli commented Jun 12, 2022

merging these notebooks @Nic-Ma @dannyhow12, please let me know any further questions.

boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
* adds 2d/3d example

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds eval

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update to use EnsureChannelFirstd

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update to use notebooks

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update to use the weekly build

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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tutorial/demo for 2D slice analysis based on 3D inputs
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