Running Pipelines on XNAT

This page provides general instructions for running any processing pipeline on XNAT. Individual pipeline pages reference this guide for the basic workflow.

General Pipeline Interface

All pipelines on XNAT follow the same basic interface through the web UI:

  1. Navigate to your project

  2. Select the subject and session

  3. Access the pipeline launcher

  4. Configure pipeline parameters

  5. Submit the job

  6. Monitor progress and results

Step-by-Step Instructions

1. Navigate to Your Data

  • Log into XNAT (https://xnat.abudhabi.nyu.edu)

  • Select your project from the project list

  • Navigate to the subject and session you want to process

2. Launch Pipeline Interface

[PLACEHOLDER - Screenshot of pipeline button location]

  • On the session page, look for the “Run Pipeline” or “Actions” button

  • Click to open the pipeline selection interface

3. Select Pipeline

[PLACEHOLDER - Screenshot of pipeline selection dropdown]

  • Choose the desired pipeline from the dropdown menu

  • Available pipelines depend on your project configuration

4. Configure Parameters

[PLACEHOLDER - Screenshot of parameter configuration interface]

  • Input Selection: Choose which scans to process

  • Output Destination: Specify where results should be stored

  • Pipeline Parameters: Set pipeline-specific options

  • Resource Allocation: Configure computing resources (if applicable)

5. Submit Job

[PLACEHOLDER - Screenshot of job submission button]

  • Review your configuration

  • Click “Submit” or “Run” to start the pipeline

  • Note the job ID for tracking

6. Monitor Progress

[PLACEHOLDER - Screenshot of job monitoring interface]

  • Check job status in the “Processing” or “Jobs” section

  • Monitor logs for progress and any errors

  • Receive notifications when job completes

Common Parameters

Input Selection: - Scan Selection: Choose specific scans to process - Session Level: Process entire session - Quality Control: Include/exclude based on QC status

Output Configuration: - Output Location: Where to store results - Naming Convention: How to name output files - Sharing Settings: Who can access results

Processing Options: - Resource Allocation: CPU, memory, time limits - Notification Settings: Email alerts for completion - Debug Mode: Enable detailed logging

Troubleshooting

Common Issues: - Permission Errors: Check project access rights - Input Validation: Ensure required scans are present - Resource Limits: Job may need more time or memory - Network Issues: Check XNAT connectivity

Getting Help: - Check pipeline logs for specific error messages - Review pipeline documentation for parameter requirements - Contact support if issues persist

Data Loss Concerns: - If you accidentally delete pipeline outputs or data, see Data Loss and Recovery for recovery options - Contact XNAT administrators immediately if critical data is lost

Next Steps

After completing this general overview: