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antonioguj / bronchinet

Airway segmentation from chest CTs using deep Convolutional Neural Networks
MIT License
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Error using the trained U-Net model #25

Open RuiqiGeng opened 2 years ago

RuiqiGeng commented 2 years ago

Hi, I am trying to use the pre-trained U-Net for my own CT data to output airway segmentation in directory "testdata/" but ran into these errors:

In FILE '/gstore/home/gengr3/BronchiNet/bronchinet/bronchinet-master/src/common/workdirmanager.py' and LINE '36': ERROR: File '/gstore/home/gengr3/BronchiNet/bronchinet/testdata//referenceKeys_posteriors.npy', does not exist... EXIT

In FILE '/gstore/home/gengr3/BronchiNet/bronchinet/bronchinet-master/src/common/functionutil.py' and LINE '185': ERROR: No files found in '/gstore/home/gengr3/BronchiNet/bronchinet/testdata//Posteriors/' with '*'... EXIT

In FILE '/gstore/home/gengr3/BronchiNet/bronchinet/bronchinet-master/src/common/functionutil.py' and LINE '185': ERROR: No files found in 'testdata//BinaryMasks/' with '*'... EXIT

What kind of data are needed in referenceKeys_posteriors.npy, Posteriors/, and BinaryMasks/?

Thanks!

id-b3 commented 2 years ago

Hello,

Can you please add more information about how you are launching the experiment? Are you using the docker image or a locally downloaded repository? What file format are your scans in?

RuiqiGeng commented 2 years ago

Hi, Thanks for your response! I am using a locally downloaded repo and the CT scans are in nii.gz. This is my tree structure:

Screen Shot 2022-07-18 at 1 52 13 PM

workDir is my work directory. The bash command I used to run the pretrained model is: bash models/run_model_trained.sh BaseData/ testdata/ --torch$

Nandayang commented 2 years ago

Same issue, anyone solve that?

dscarmo commented 1 year ago

Is this because the models are on git lfs maybe?

m5b6 commented 10 months ago

Same issue here

hwjung92 commented 2 weeks ago

When using the pre-trained model, it shows the same error.

============================================================================== bash models/run_model_trained.sh Data/Images Data/Results --torch

In FILE '/home/user/MIA_Project/bronchinet/src/common/workdirmanager.py' and LINE '36': ERROR: File '/home/user/MIA_Project/bronchinet/Data/Results/referenceKeys_posteriors.npy', does not exist... EXIT

Where Can I find the file (referenceKeys_posteriors.npy) ?