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BHICP Software: how to use

1) System requirements

  • Mac OS X 64-bit (Software for other Unix-based machines on the way)

2) Installation

Download the required files from the BHICP Software page. From terminal, move to the BHICP folder and run the included Makefile with:

 $ make 

This should create the executable file CoxClusterProcess.

3) Running the software

Input files

The following input files are required:

  • <data_name>.dat: The file containing the foci coordinates.
  • newpars.txt: The file containing simulation details: prior distributions, MCMC running time, etc.
  • seed.dat: The file containing the seed for random number generations.

Data format

The following guidelines must be taken into consideration when generating the data file containing the foci:

  • The file consists of 5 columns.
  • The first column contains the study (contrast) ID number, ranging from 1 to the total number of studies in the sample.
  • Columns 3,4 and 5 contain the x,y and z coordinates of the focus, always in MNI voxel space. Since 2mm voxels are used, columns 2 and 4 should range between 1 and 91, while column 4 should range from 1 to 109.
  • Column 5 contains the study type number. If no discrimination between types is done, set column 5 to one.

Overall the file should look like:


Once all input files are created, type the following command in terminal to execute the software:

 $ ./CoxClusterProcess <results_folder> <data_name>.dat newpars.txt


  • <results_folder> is the subfolder of folder simresults where posterior draws will be stored
  • <data_name>.dat is the file containing the foci
  • newpars.txt: is the file containing the simulation details

4) Results

All the results are stored in the directory .../BHICP/simresults/<results_folder>. A detailed description of the output files generated during execution will become available soon.