I am looking for some advice on how to effectively use our HPC cluster. Our HPC cluster only has temporary storage for data processing. It is intended to be used for batch processing and not for interactive data processing or data visualization. Our data is stored on a separate computer and network disk space.  With this setup I was planning to do the following

1) rsync data from network disk to HPC cluster temporary storage
2) Process each subject indivudally via conn_batch (preprocessing, setup, denoising, and first level analysis)
3) rsync_data from HPC cluster temporary storage back to our permanent network disk
4) merge individual subjects into a single project
5) perform second level analysis.

For 64 subject with pre and post scans, I am able to do steps 1-3 in about an hour (15 minutes setup, 45 minutes computer time). And although this processing stream may not be ideal it works for me. 

The problem I am have is with merging the files.  Since individual folders created by CONN have moved Conn needs to confirm the location of the individual's data and the location of the ROIs.  Doing this manually takes me about 1-2 minutes per subject.  This adds about 1 to 2 hours of just clicking buttons. 

Is there anyway to automate this process in CONN? 

Thanks for your help,

Bob