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MIC-DKFZ / nnUNet

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why the dice is 0 or nan #2034

Closed 2345678y3 closed 4 months ago

2345678y3 commented 6 months ago

屏幕截图 2024-03-24 090414 thank you

MD7sjh commented 5 months ago

I have encountered your problem before, can you describe your situation in detail.

2345678y3 commented 5 months ago

My dataset is segmentation of brain metastases, and my labels may have 1 2 3 ... The maximum number of labels is 42, the size of the label voxels is different, the dataset size is 344 cases, the loss cannot converge to -0.1 after training with nnunetv2, and there are many 0s and nans in each enpoch and in dice, and the final training of the model，the dice progress is only 0.03

2345678y3 commented 5 months ago

I have encountered your problem before, can you describe your situation in detail.↳

What is the reason for your situation?thank you

2345678y3 commented 5 months ago

I have tried the nnUNetTrainerDiceCELoss_noSmooth but the problem hasn't been solved yet.

Karol-G commented 5 months ago

Dear @2345678y3,

Thank you for using nnU-Net.

To assist you better, we need a clearer understanding of the issue you're encountering. It appears there might be some confusion regarding your problem or the specific outcomes you aim to achieve with nnU-Net.

Could you please provide a more detailed description of your task and the problems you have encountered? This information will greatly aid us in identifying potential solutions.

In addition, we require the following specific information to proceed with a thorough investigation:

These details are crucial for us to understand the context and specifics of your setup, which in turn will help us provide you with targeted support.

We appreciate your cooperation and look forward to your response.

Best regards,

Karol Gotkowski

2345678y3 commented 5 months ago

杨钦 @.***

 this is my training code and the result,thank you 

------------------ 原始邮件 ------------------ 发件人: "MIC-DKFZ/nnUNet" @.>; 发送时间: 2024年4月2日(星期二) 下午4:24 @.>; @.**@.>; 主题: Re: [MIC-DKFZ/nnUNet] why the dice is 0 or nan (Issue #2034)

Dear @2345678y3,

Thank you for using nnU-Net.

To assist you better, we need a clearer understanding of the issue you're encountering. It appears there might be some confusion regarding your problem or the specific outcomes you aim to achieve with nnU-Net.

Could you please provide a more detailed description of your task and the problems you have encountered? This information will greatly aid us in identifying potential solutions.

In addition, we require the following specific information to proceed with a thorough investigation:

The dataset.json file and the exact preprocessing, train, and inference commands you used.

Training images and their respective ground truth. For confidentiality and review purposes, you can post screenshots or send full examples to @.*** via cloud storage. Rest assured, any data received will be treated with the utmost confidentiality and will be deleted after the review.

The training log and the progress.png for every fold, compiled into a zip archive.

These details are crucial for us to understand the context and specifics of your setup, which in turn will help us provide you with targeted support.

We appreciate your cooperation and look forward to your response.

Best regards,

Karol Gotkowski

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

Karol-G commented 5 months ago

Hey,

You did not send any additional information. Please review your reply again. Thank you.

Best regards, Karol

MD7sjh commented 5 months ago

Have you ever changed your network architecture？My situation is I change the network, it can not read my dataset properly in my inference stage.

2345678y3 commented 5 months ago

Hey,

You did not send any additional information. Please review your reply again. Thank you.

Best regards, Karol

i have sent it to you again，could you take a look again? thank you !

2345678y3 commented 5 months ago

Hey,

You did not send any additional information. Please review your reply again. Thank you.

Best regards, Karol

mynnuet.zip

deepsea6034625 commented 5 months ago

I also saw same result. Dice was 0.01 and and see too man "nan" at the result.

Karol-G commented 4 months ago

Hey @2345678y3,

According to your dataset.json your dataset has 42 different tumor classes. Are you sure this is correct? A class label separates usually different concepts such as different organs or different regions of the same tumor. It seems to me that your dataset has in total 42 tumor instances and that you assigned a class to each instance. Can you explain your task a bit more and comment on if my assumption is right?

Best, Karol

deepsea6034625 commented 4 months ago

Sorry, Dataset was about teeth segmentation. Label is like as follow: 0: background 1~16: upper teeth 17~32: lower teeth. This is just instance segmentation project. But unfortunately, nnUNet was just semantic segmentation. I want to separate individual tooth from CBCT 3D image. I already segmented upper teeth component and lower teeth component but have no idea how to separate individual ones. If you have good idea, please tell me. Thank you.

2345678y3 commented 4 months ago

Thank you for your answer，sir .My dataset is brain metastasis ,so,one patient  may have more than one metastasises that from the same tumor in his brain,thus,if the person has 42 metastasises in his brain,i will label every metastasis  with different labelname。so i should label them with the same label right?

发自我的iPhone

------------------ Original ------------------ From: Karol Gotkowski @.> Date: Mon,May 6,2024 8:01 PM To: MIC-DKFZ/nnUNet @.> Cc: 2345678y3 @.>, Mention @.> Subject: Re: [MIC-DKFZ/nnUNet] why the dice is 0 or nan (Issue #2034)

Karol-G commented 4 months ago

@deepsea920415 Please open a separate issue for your problem. It is different to this issue opened by @2345678y3 . Thank you.

deepsea6034625 commented 4 months ago

Already done.(CBCT teeth segmentation) But couldn't get any good idea.

Karol-G commented 4 months ago

Hey @2345678y3,

Yes, exactly nnunet is not capable of doing instance segmentation. It can only do semantic segmentation. So in your case, it seems there is only one class which would be the class "Metastasis".

Best, Karol

2345678y3 commented 4 months ago

thank you for your help  sir

发自我的iPhone

------------------ Original ------------------ From: Karol Gotkowski @.> Date: Mon,May 6,2024 8:47 PM To: MIC-DKFZ/nnUNet @.> Cc: 2345678y3 @.>, Mention @.> Subject: Re: [MIC-DKFZ/nnUNet] why the dice is 0 or nan (Issue #2034)

Hey @2345678y3,

Yes, exactly nnunet is not capable of doing instance segmentation. It can only do semantic segmentation. So in your case, it seems there is only one class which would be the class "Metastasis".

Best, Karol

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

yibeizixia commented 4 months ago

Have you solved the issue yet? I'm facing the same problem as well.

Karol-G commented 4 months ago

@yibeizixia Please open a separate issue for your problem as it is most likely not related to @2345678y3