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Fixes # .

Description

Tutorial for using e2e-VarNet for MRI reconstruction.

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

mersad95zd and others added 19 commits July 31, 2022 13:39
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
… inference.ipynb

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
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@mersad95zd mersad95zd marked this pull request as ready for review September 7, 2022 21:05
@Can-Zhao
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Can-Zhao commented Sep 9, 2022

Could you remove the redundant files like fastmri_ssim.py? You could provide a link in the tutorial readme.

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Can-Zhao commented Sep 9, 2022

  1. Please put data_split file in json format, and send it to Wenqi. He will upload it to some link. In your readme, you just need to add the download link.
  2. In Dataset section, could you explain the data path in the folder, e.g., "download the file XXX to ./data"?
  3. Let U-net demo and Varnet-demo share the same Dataset section, e.g. "The data preparation is explained in ../unet_demo"

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Can-Zhao commented Sep 12, 2022

I just realized your U-net demo does not use train/val/test split, but instead test on validation set. Could you change it to train/val/test as in varnet demo? Please them share the same data split so the users can compare the performance better. Thanks!

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@wyli wyli merged commit de12b79 into Project-MONAI:main Sep 13, 2022
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
* initial unet recon demo commit

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fixed formatting errors

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fixed formatting errors

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fixing formatting errors

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* more experimental details added

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* removed checkpoint from this PR; minor fix to checkpoint directory in inference.ipynb

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* clarified common practice for fastMRI inference

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fixed model checkpoint name in all files

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* added model checkpoint link to readme

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* init varnet commit

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* back to init commit

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* updated readmes

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* removed unet files

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* updated inference files based on the data split

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* minor update to unet inference

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
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3 participants