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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

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  
  - ./RunMe.sh <lesionmask> <threshold> <manualmask> <foldershortname> <modelname> <distancefunction>  <factor>  <symmetry>  <weight>  <p_norm> <saveoutput>
  or
  - bash  RunMe.sh <lesionmask> <threshold> <manualmask> <foldershortname> <modelname> <distancefunction>  <factor>  <symmetry>  <weight>  <p_norm> <saveoutput>
```