Welcome to DAX’s documentation!

DAX is Distributed Automation for XNAT

DAX allows you to:

• store analyzed imaging data on XNAT (datatypes)

• extract information from XNAT via scripts (Xnat_tools)

• run pipelines on your data in XNAT via a cluster (processors)

Installation

To install please reference our Install Page

Contents:

• Installing DAX in a Virtual Environment
  • Table of Contents
    • Setup
    • Create the Virtual Environment
    • Install DAX
    • Verify Installation
• Installation of fs:fsData and proc:genProcData
  • On XNAT VM:
  • ON XNAT webapp:
• Source Documentation
  • dax – Root package
  • dax.task – Task class
    • ClusterTask
    • Task
    • XnatTask
  • dax.spiders – Spider class
  • dax.processors – Processor class
    • AutoProcessor
    • Processor
  • dax.log – Logging utility
    • setup_critical_logger()
    • setup_debug_logger()
    • setup_error_logger()
    • setup_info_logger()
    • setup_warning_logger()
  • dax.bin – Responsible for launching, building and updating a Task
    • build()
    • check_default_keys()
    • launch_jobs()
    • load_from_file()
    • raise_yaml_error_if_no_key()
    • read_yaml_settings()
    • set_logger()
    • undo_processing()
    • update_tasks()
  • dax.XnatUtils – Collection of utilities for upload/download and general access
    • AssessorHandler
    • CachedImageAssessor
    • CachedImageScan
    • CachedImageSession
    • CachedResource
    • InterfaceTemp
    • SpiderProcessHandler
• DAX Manager
  • Table of Contents:
    • About
    • How to set it up
  • DAX 1
    • How to add a Module in DAX 1
    • How to add a Process in DAX 1
  • LDAX
    • How to add a Module in LDAX
    • How to add a Process in LDAX
• Contributors
• How To Contribute
• FAQ
• DAX Processors
  • About
  • Processor Repos
  • Overview
  • A “Simple” Example
  • Parts of the Processor YAML
  • inputs
    • xnat scans
    • xnat assessors
    • xnat attrs
    • xnat filters
    • outputs
    • command
    • attrs
    • jobtemplate
  • Versioning
  • Notes on Singularity run options
• DAX Processors, version 3
  • About
  • Processor Repos
  • Overview
  • A Basic Example
  • Parts of the Processor YAML
  • inputs (required)
    • xnat scans
    • xnat assessors
    • xnat attrs
    • xnat filters
    • outputs
    • command
    • jobtemplate
  • Versioning
  • Notes on singularity options
  • Subject-Level Processors
• Assessors in VUIIS XNAT
• DAX Command Line Tools
  • Table of Contents
  • List of the Tools
    • XnatSetup
    • XnatQuery
    • XnatCheck
    • XnatDownload
    • XnatUpload
    • XnatReport
    • XnatSwitchProcessStatus
    • XnatProcessUpload
    • XnatSubjectUpdate
    • RedCapReport
    • XnatCheckLogin
    • Xnatinfo
    • Xnatsessionupdate
    • BIDSMapping
    • XnatBOND
• DAX Executables
  • Table of Contents
    • DAX Packages
  • How Does it Work?
  • DAX Settings
  • How to Write a ProjectSettings.yaml File
    • DAX Executables
  • DAX Build
  • DAX Update
  • DAX Launch
  • DAX Upload
  • DAX Manager
• Manage a Project
  • Table of Contents
    • Check Why an Assessor Failed
    • Set/Reset Assessors to Run
    • Run an XnatCheck on Your Project
    • Run dax_update Manually on a Project (Advanced Users)
    • Run dax_launch Manually on a Project (Advanced Users)
    • Common and Spurious Errors You May Encounter
  • Unable to Read Experiments for Project: XXXXXXXX
  • Restarting a Job
  • Project Settings Files
  • Adding Directories Caused by OSError (only relevant to LDAX)
  • Settings Directory is Missing from tmp Folder (only relevant to LDAX)
  • Verifying the Spider is Waiting to get Uploaded to XNAT
• BIDSMapping: Walkthrough Tutorial
  • Introduction
  • Table of Contents
    • Step 1 Mapping Datatype and Scans
    • Step 2 Upload Datatype Mapping to XNAT
    • Step 3 Check Project Level File Manager
    • Step 5 Upload Tasktype Mapping to XNAT
    • Step 6 Upload Repetition Time Mapping to XNAT
    • Step 7 Upload Repetition Time Mapping to XNAT
    • Step 8 Check Project Level File Manager
    • Step 9 Mapping Perfusion Imaging Type
    • Step 10 Upload Perfusion Type to XNAT
    • Step 11 Check Project Level File Manager
  • Additional Useful BIDSMapping Tool Options
    • Step 12 Correct Old Mapping
    • Step 13 Replace Existing Mapping
    • Step 14 Check Corrected LOGFILE
    • Step 15 Add New Mapping
    • Step 16 Update Existing Mapping
    • Step 17 Check Updated LOGFILE