Running Subjects on SGE - McIntosh-Lab/tvb-ukbb GitHub Wiki

This page contains instructions for running subjects through the TVB-UKBB pipeline on Sun Grid Engine (SGE) systems. Note that you will likely need to customize the pipeline to your dataset.

Running

Following the installation example above,

  1. Source the file init_vars to activate the conda environment and define environment variables. For example, if your pipeline is located at /home/username/tvb-pipeline/, simply run

. /home/username/tvb-pipeline/tvb-ukbb/init_vars

and your environment will be loaded.

  1. cd to the directory containing your subject directory, e.g., subjDir.

  2. Run a subject with

python /home/username/tvb-pipeline/tvb-ukbb/bb_pipeline_tools/bb_pipeline.py subjDir

Please note that if you'd like to re-process an previously processed subject (including failed processing), you will need to clear your subject's folder so that it only contains the rawdata subdirectory. The exception for this requirement is when reparcellating, in which case the subject folder can be left intact.

  1. Monitor the progress of your subject by cding to subjDir/logs.

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