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CAMP-TUM network contributions: Quicknat and Daf3D (Project-MONAI#6306)
Fixes Project-MONAI#5921 ### Description @Al3xand1a and @ge96lip implement DAF3D[1] and Quicknat[2] networks and test them in open-source and local datasets. We use as a baseline the pytorch codes available in [3] and [4] We are quite confident about the implementation, but feel free to contact us if you find errors. For any questions send us an email to ge45qix@mytum.de We have some questions for the contribution: For Quicknat: 1) we add the sequential class file in the networks folder because we do not know where to add it. 2) How do we include the squeeze and excitation requirement (sse and Csse) if it comes from a GitHub repository? https://github.com/ai-med/nn-common-modules/releases/download/v1.1/nn_common_modules-1.3-py3-none-any.whl For Daf3D 3) Are the overwritten blocks fine as they are? or do they have to be more flexible? For both: We run this command line (`./runtests.sh --quick --unittests --disttests`) but the error we are getting is not related to our changes, so we run our unit_test independently and they work. Same with documentation. [1] Deep Attentive Features for Prostate Segmentation in 3D Transrectal Ultrasound. Yi Wang, Haoran Dou, Xiaowei Hu, Lei Zhu, Xin Yang, Ming Xu, Jing Qin, Pheng-Ann Heng, Tianfu Wang, and Dong Ni. IEEE Transactions on Medical Imaging, 2019. [2] 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. [3] https://github.com/ai-med/quickNAT_pytorch [4] https://github.com/wulalago/DAF3D ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: ge96lip <73938628+ge96lip@users.noreply.github.com> Signed-off-by: vanessagd.2395 <vanessa.gonzalez-duque@eleves.ec-nantes.fr> Signed-off-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com> Co-authored-by: Alexandra Marquardt <alexandra@MBPvonAlexandra.fritz.box> Co-authored-by: Carlotta <carlotta.hoelzle@icloud.com> Co-authored-by: Alexandra Marquardt <alexandra@w223-2e-v4.eduroam.dynamic.rbg.tum.de> Co-authored-by: Vanessa <vanessa.gonzalezduque@ls2n.fr> Co-authored-by: ge96lip <73938628+ge96lip@users.noreply.github.com> Co-authored-by: “Vanessa <“vanessa.gonzalezduque@ls2n.fr”> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alexandra Marquardt <alexandra@w192-1i-v4.eduroam.dynamic.rbg.tum.de> Co-authored-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com> Co-authored-by: Alexandra Marquardt <alexandra@w217-4n-v4.eduroam.dynamic.rbg.tum.de>
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