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Samuel Callahan
SCallahan/
CNN-Diffusion-MRIBrain
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### Tests





  
  

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[pipeline_test.sh](./pipeline_test.sh) is a convenient testing infrastructure.





  
  

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In addition to the prerequisites mentioned in [instructions](../docs/README.md#installation),





  
  

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it is depdendent on the following executables:





  
  

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* dcm2niix





  
  

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* fslroi





  
  

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* bet





  
  

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* antsRegistrationSyNQuick.sh





  
  

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We recommend only putting the above executables in `PATH` without sourcing extenal environments





  
  

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such as FSL's. For example--`fslroi`, `bet` could be put in `PATH` as:





  
  

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> export PATH=/path/to/fsl-6.0.7/share/fsl/bin:$PATH





  
  

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In addition, you need to set:





  
  

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```





  
  

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export FSLDIR=/path/to/fsl-6.0.7/





  
  

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export FSLOUTPUTTYPE=NIFTI_GZ





  
  

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```





  
  

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Moreover, you can put an `exit` statement after any line between 70-81 to run one or more tests:





  
  

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https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/blob/a81ef7e939714f88b67c0a6e84a0ff6db7004622/tests/pipeline_test.sh#L70-L81





  
  

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