How to use the pretrained Synapse weight to test my own dataset?

[qingwang-usc]

Dear Authors:
Hello, now I have some abdomen data, I want to load the pre-training Synapse weight directly and then test my data, but I don't know how to do it, could you tell me the approximate steps of testing my own data, thank you very much!

[Amshaker]

Hi @qingwang-usc ,

Sorry for the late reply.

To do that, please follow the following steps:-

1- You have to do the preprocessing of nnFormer. Mainly, you have to divide your data into 3D slices of size 128x128x64. Then, apply the same transformation of nnFormer.

2- After the data is pre-processed and ready, you may follow the scripts inside: https://github.com/Amshaker/unetr_plus_plus/blob/main/evaluation_scripts/run_evaluation_synapse.sh and replace the evaluation samples of Synapse by your pre-processed data and run the same script. Alternatively, you can adopt https://github.com/Amshaker/unetr_plus_plus/blob/main/unetr_pp/inference/predict_simple.py to load your pre-processed data, our Synapse architecture, and the checkpoint of Synapse, and do the prediction for your pre-processed data.

I hope my answer gives you an overview of the steps you needed.

Please let me know if you have other questions.

Best regards,
Abdelrahman.

[qingwang-usc]

Thanks a lot！

…

---Original--- From: "Abdelrahman ***@***.***> Date: 2023/6/2 08:27:20 To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [Amshaker/unetr_plus_plus] How to use the pretrained Synapseweight to test my own dataset? (Issue #28) Hi @qingwang-usc , Sorry for the late reply. To do that, please follow the following steps:- 1- You have to do the preprocessing of nnFormer. Mainly, you have to divide your data into 3D slices of size 128x128x64. Then, apply the same transformation of nnFormer. 2- After the data is pre-processed and ready, you may follow the scripts inside: https://github.com/Amshaker/unetr_plus_plus/blob/main/evaluation_scripts/run_evaluation_synapse.sh and replace the evaluation samples of Synapse by your pre-processed data and run the same script. Alternatively, you can adopt https://github.com/Amshaker/unetr_plus_plus/blob/main/unetr_pp/inference/predict_simple.py to load your pre-processed data, our Synapse architecture, and the checkpoint of Synapse, and do the prediction for your pre-processed data. I hope my answer gives you an overview of the steps you needed. Please let me know if you have other questions. Best regards, Abdelrahman. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>