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# performance_analysis

This software/script  calculates all the following important performance metrics:
- Dice Similarity Index (SI) 
- Sensitivity  
- Precision  
- Specificity 
- Jaccardindex  
- Conformity 
- HausdorffDistance
- Overlapcoefficient 
- Tanimotocoefficient
- Matthewscorrelationcoefficient  
- Accuracy 
- Voxel-level False Discovery Rate (FDR) 
- Voxel-level False Negative Ratio (FNR)
- Cluster-level FDR 
- Cluster-level FNR 
- Detection Error Rate (DER) 
- Outline Error Rate (OER)
- Mean Total Area (MTA)
- Volume of segmentation
- Volume of manual mask

# Running the Program!

Use one of the following methods to run the program:

(1) Using shell script file "RunMe.sh" which can be run by the Unix shell

```sh
  - chmod 755 RunMe.sh  
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  - ./RunMe.sh <lesionmask> <threshold> <manualmask> <foldershortname> <modelname> <distancefunction> <factor/operation> <symmetry> <weight> <p_norm> <saveoutput>
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  or
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  - bash  RunMe.sh <lesionmask> <threshold> <manualmask> <foldershortname> <modelname> <distancefunction> <factor/operation> <symmetry> <weight> <p_norm> <saveoutput>
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```  
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where
```sh
 - <lesionmask>: Segmented lesion mask using lesion prediction algorithm
 - <threshold>:  Probability threshold that will be applied to  output before calculation of the overlap measures
 - <manualmask>:  The manual segmentation 
 - <foldershortname>
 - <modelname> 
 - <distancefunction> 
 - <factor/operation> 
 - <symmetry> 
 - <weight> 
 - <p_norm> 
 - <saveoutput>
```
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