jiyuanfeng / amos Goto Github PK

When processing ct data, run "nnUNet_convert_decathlon_task -i ./DATASET/AMOS22_raw/AMOS22_raw_data/Task01_AMOS_CT
nnUNet_plan_and_preprocess -t 1", you will get two files: nnUNetData_plans_v2.1_stage0 and nnUNetData_plans_v2.1_stage1, but I found that there are 600 files in nnUNetData_plans_v2.1_stage0, including 300 .npz files and 300 .pkl files, which is consistent with the number of CT images, but there are only 326 files in total in nnUNetData_plans_v2.1_stage1. Is this normal?

Would you mind introuducing whether and when would you release the training and inferfence codes?
Many thanks.

Hii,

I appreciate your effort in releasing the code. Could you please provide the details necessary to reproduce the cross-modality learning results (CT-MRI: 80.56, MRI-CT: 79.97) reported in section 4.4 of your paper?

Thank you.

Hi could you please tell me how long it takes for training on ct task. I trained it on TITAN with 12 G memory, and it takes about 11 days which is too long

Hello, where is the code for reproducing the result?

Great code and very impressive paper. Thank you very much!

I am writing to consult problem with transfer learning from AMOS dataset to KiTS dataset.

In the table 3 of the paper, you pre-trained with AMOS, then apply it on KiTS dataset, finally, you got 88.33 dice score, I found it is very interesting, so I tried the same thing, but only got 65.54 dice score. I don't know what is went wrong, the following is the potential problem:

1. The two dataset has different axis ordering, AMOS dataset is (z,y,x), while KiTS is (x,y,z). Did you doing anything to preprocess it or you just ignore it?
2. The two dataset has different voxel spacing, how did you preprocess them to become same target spacing?

Hope to get some response from you. Thank you~

What's meaning of 'prostate/uterus'? It means "prostate and uterus" or "prostate or uterus"?

Hello,

Thanks for your work.
Could you please tell me what is the latest dataset license?

• CC BY-NC-SA license?
• Creative Commons Attribution 4.0 International license?
• Or other licenses?

https://github.com/JiYuanFeng/AMOS/blob/90d506ea97d0bef2e9b5304b6bdbc45c047aa327/nnunet/experiment_planning/utils.py#L52C28-L52C28
Should I use nnUNet_raw_data instead of temp？

Thank you so much for the valuable abdominal multi-organ data and for hosting the AMOS2022 competition.
I am currently training with the Amos 2022 data set.
Could you tell me how to submit the test set after the competition?

I know to submit the test set file on this page, may I ask what the submission file is TEAMNAME.tar.gz？
But obviously not, it will alert me to file format errors, so I am very anxious that you will see my question and reply as soon as you can.
Finally, thank you very much for your hard work！

Hi,
Excellent dataset and paper. I'd like to use AMOS for my research and want to reproduce some results in the paper. But I find that codes are removed from this repo. I would greatly appreciate it if you could provide some code to help me get started.

Best.