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README.md

GingerALE

GingerALE is the BrainMap application that is used to perform an ALE meta-analysis on coordinates in Talairach or MNI space. GingerALE can also be used to convert coordinates between MNI and Talairach spaces using the icbm2tal transform.

See more at http://www.brainmap.org/ale/

Single core example

  • Login to the SCW cluster.

  • Create a new directory called ginger_ale.

    mkdir ~/ginger_ale && cd $_

  • Download the SCW single core GingerALE example.

    wget https://github.com/BangorUniversity/Research-Computing-Community/raw/master/tutorials/neuroimaging/ginger_ale/examples/GingerALE.zip

  • Extract the archive.

    unzip GingerALE.zip
cd GingerALE

  • Change the account code to your SCW project code.

    nano run.slurm

#SBATCH --account={{insert your project code}}
    • To exit nano press 'ctrl + x' and press 'y' to save changes.

  • Submit the job request to the slurm scheduler.

    sbatch run.slurm

  • Check the status of your jobs in the queue.

    watch squeue --user=$USER
    • Press 'ctrl + c' to exit the 'watch' program.

  • Once the job has finished, output results are available in the same directory as the job submission file.

    • To run multiple GingerALE jobs in parallel, see below.

GingerALE and GNU Parallel

  • TODO