Some potential problems with solution

[vigor-jzhang]

Thanks for sharing this code and pretrained weights! It is very helpful to my project.

When I try to run inferencing with provided code, some errors happened, and I spent several hours to solve them. I list here for authors to modify code / modify instructions, and also hope this post will be useful for other guys interested in this code.

1. Project is based on nnUNet v1, the right url is https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
2. After installation, replace the './nnUNet/nnunet' folder with this repository 'src/nnunet', which contains the needed python codes.
3. missing plans.pkl: copy from 'nnUNet_preprocessed/Task111_PancreasT2MRI/nnUNetPlansv2.1_plans_3D.pkl" to "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/plans.pkl"
4. missing postprocessing.json: copy from
   "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/fold_0/postprocessing.json" to "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json"
5. May facing error with "No module named '_tkinter'": comment Line 9 [from turtle import forward] of "nnunet/network_architecture/custom_modules/post_embeddings.py"

[ulasbagci]

Thank you! Zheyuan ?

…

On Tue, Aug 27, 2024, 11:22 PM Jianwei Zhang ***@***.***> wrote: Thanks for sharing this code and pretrained weights! It is very helpful to my project. When I try to run inferencing with provided code, some errors happened, and I spent several hours to solve them. I list here for authors to modify code / modify instructions, and also hope this post will be useful for other guys interested in this code. 1. Project is based on nnUNet v1, the right url is https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1 2. After installation, replace the './nnUNet/nnunet' folder with this repository 'src/nnunet', which contains the needed python codes. 3. missing plans.pkl: copy from 'nnUNet_preprocessed/Task111_PancreasT2MRI/nnUNetPlansv2.1_plans_3D.pkl" to "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/plans.pkl" 4. missing postprocessing.json: copy from "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/fold_0/postprocessing.json" to "nnUNet_trained_models/nnUNet/3d_fullres/Task111_PancreasT2MRI/nnTransUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json" 5. May facing error with "No module named '_tkinter'": comment Line 9 [from turtle import forward] of "nnunet/network_architecture/custom_modules/post_embeddings.py" — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEB2UFW36M2WHOOO5NAHX2TZTT34FAVCNFSM6AAAAABNHBB3HGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4TANBXGAZTSMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[freshman97]

This is a really great suggestion, and I will merge them accordingly. The plans.pkl files have been uploaded, and the postprocessing.json has also been merged.

I will also keep this issue open as one guide for future people.