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)
Quick Install¶
Create a python3 virtual environment with dax and all dependencies.
python3 -m venv daxvenv
source daxvenv/bin/activate
pip install dax
Configure an environment variable named XNAT_HOST set to the full url of your xnat server. This can be incuded in your .bashrc/.bash_profile file.
export XNAT_HOST=https://central.xnat.org
Configure your credentials in a file named “.netrc” in your home directory.
machine <SERVER>
login <USER>
password <PASSWORD>
Here SERVER is the server name only. For example, central.xnat.org, not https://xnat.website.com/xnat.
Versions and Installation¶
Our currently running versions of dax are:
Dax 2 - 2.2.1 - As of July 8, 2021
Used for most purposes
LDAX latest - 0.7.10 - As of October 7, 2020
Legacy Dax - Please use DAX 2
These can be verified with
dax version
# or
pip freeze | grep dax
# or
python3 -m pip freeze | grep dax
To install please reference our Install Page
Contents:
- Installing DAX in a Virtual Environment
- Installation of fs:fsData and proc:genProcData
- Source Documentation
- DAX Manager
- Contributors
- How To Contribute
- FAQ
- DAX Processors
- DAX Processors, version 3
- Assessors in VUIIS XNAT
- DAX Command Line Tools
- DAX Executables
- Manage a Project
- 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