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CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://www.cbica.upenn.edu/captk
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DeepMedic won't run in singularity container #1516

Open Bananahopper opened 10 months ago

Bananahopper commented 10 months ago

Describe the bug When running DeepMedic in a container on a cluster with singularity, I get the following error :

Starting DeepMedic Segmentation. sh: /work/CaPTk/bin/deepMedicInference: Is a directory DeepMedic exited with code !=0. Something went wrong when performing skull-stripping using DeepMedic, please re-try or contact sofware@cbica.upenn.edu.

I get this error when running DeepMedic by itself or through the BraTSPipeline.

To Reproduce Steps to reproduce the behavior:

  1. Pull container from dockerhub with singularity pull docker://cbica/captk:{version}
  2. Run container (interactive or not) with command /work/CaPTk/bin/DeepMedic -md /work/CaPTk/bin/../data//deepMedic/saved_models/skullStripping/ -i /output//T1_to_SRI.nii.gz,/output//T1CE_to_SRI.nii.gz,/output//T2_to_SRI.nii.gz,/output//FL_to_SRI.nii.gz -o /output//dmOut_skull/brainMask_SRI.nii.gz
  3. See error

Expected behavior DeepMedic doesn't get stuck and gives an output

Screenshots If applicable, add screenshots to help explain your problem.

CaPTk Version azure-latest, but also in latest and all previous containers

HPC: fedora 8.6

Additional context In the BraTSPipeline everything before the DeepMedic segmentation runs without issue as intended.