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TUM-CAMP-tutorials-contribution: DAF3D and Quicknat #1440
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mingxin-zheng commented on 2023年06月28日T07:15:46Z
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Thank you for the PR. According to our contributing guideline we would need a "Setup imports" instead of "Preprocess the data in folders" here.
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mingxin-zheng commented on 2023年06月28日T07:15:48Z
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Line #13. image_path_expression = "PROCESSED/MPRAGE/T88_111/OAS1_*_MR*_mpr_n*_anon_111_t88_masked_gfc.img"
Is the path correct? It seems the runner is complaining about not finding the files:
IndexError Traceback (most recent call last)681
Input In [4], in <cell line: 2>()682
14 segmentation_path_expression = "FSL_SEG/OAS1__MR_mpr_n*_anon_111_t88_masked_gfc_fseg.img"683
15 image_paths = glob(os.path.join(data_dir, "*", image_path_expression))684
---> 16 print(image_paths[0])685
17 image_paths += glob(os.path.join(data_dir, "/", image_path_expression))686
18 segmentation_paths = glob(os.path.join(data_dir, "*", segmentation_path_expression))687
688
IndexError: list index out of range
For more details, this can be found in:
TUM-CAMP-tutorials-contribution: DAF3D and Quicknat · Project-MONAI/tutorials@fd221ce (github.com)
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mingxin-zheng commented on 2023年06月28日T07:15:49Z
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Line #5. lossFunction = DiceCELoss(include_background=True, to_onehot_y=True, softmax=True)
Please check the PEP 8 error regarding the variable naming:
TUM-CAMP-tutorials-contribution: DAF3D and Quicknat · Project-MONAI/tutorials@fd221ce (github.com)
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mingxin-zheng commented on 2023年06月28日T07:15:51Z
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Line #1. num_epochs = 20
We typically use max_epochs to control the notebook running pipeline (build). For more details, please refer to our contributing guide: https://github.com/Project-MONAI/tutorials/blob/main/CONTRIBUTING.md#notebook-execution
Signed-off-by: Alexandra Marquardt <alexandra@MacBook-Pro-von-Alexandra.local>
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...into TUM-CAMP-tutorials
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Nic-Ma
commented
Jul 24, 2023
Hi @vgonzalezd ,
As the module had been merged into MONAI core, could you please help update and complete this PR?
Thanks in advance.
smith-kyle
commented
Jan 31, 2024
Just a heads up, you can review notebook changes like this using GitNotebooks.
e.g. this pull request https://gitnotebooks.com/Project-MONAI/tutorials/pull/1440
It allows inline comments on code and markdown, and it's free for public repos so I thought I'd share..
Fixes # .
Description
@Al3xand1a and @ge96lip create these 2 tutorials for 2 networks that were recently accepted in MONAI core:
DAF3D[1] and Quicknat[2]
We would like to have your feedback to improve the contribution. Thank you in advance!
For any questions send us an email to ge45qix@mytum.de
[1]DAF3D:
Wang, Y., Dou, H., Hu, X., Zhu, L., Yang, X., Xu, M., ... & Ni, D. (2019). Deep attentive features for prostate segmentation in 3D transrectal ultrasound. IEEE transactions on medical imaging, 38(12), 2768-2778.
https://github.com/wulalago/DAF3D/blob/master/README.md
[2]QuickNAT:
Roy, A. G., Conjeti, S., Navab, N., Wachinger, C., & Alzheimer's Disease Neuroimaging Initiative. (2019). QuickNAT: A fully convolutional network for quick and accurate segmentation of neuroanatomy. NeuroImage, 186, 713-727.
https://www.sciencedirect.com/science/article/abs/pii/S1053811918321232
Checks
./figurefolder./runner.sh -t <path to .ipynb file>