Command Line: BSE

Forums Forums Cortical Surface Extraction Command Line: BSE

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    • #345
      wwu94
      Participant

      Hi,

      I am trying to use the skull stripping tool through command line in Linux system. According to the website: the code should be bse -i input [optional settings]

      However, I am not sure how to start all this and when I typed in bse. Terminal shows that there is no such command.

      Thanks for helping!

    • #350
      David Shattuck
      Keymaster

      Hello –

      To run bse from the command line, you need to either specify the path to the bse command or add the path to your PATH variable. For example, if you unpacked the BrainSuite programs to your home directory, which I’ll call wwu94, then the path would be:

      /home/wwu94/BrainSuite16a1/bin

      In Linux BASH, you can type this command:

      export PATH=/home/wwu94/BrainSuite16a1/bin:$PATH

      to add BrainSuite’s program directory to the start of your path. Then, when you call bse, it should run.

      You can also call the programs on the command line like this:

      /home/wwu94/BrainSuite16a1/bin/bse

      which tells the shell the precise location of the program.

      Please give that a try.

      thanks,
      David Shattuck

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