xnattools

xnattools is a python package for handy operations on XNAT data.

Documentation

The complete documentation is available at https://radiology.gitlab.io/radiomics/xnattools/ . The following example is a small part of tutorials. Please refer to the documentation for additional tutorials, examples, how-to guides, and developer guides.

Prerequisites

Before you begin, make sure you have:

1. Installed xnattools. For example using pip:

   pip install xnattools
   

2. Set up your XNAT credentials using one of these methods:

   Option 1: Using .netrc file (recommended)

   Create or edit ~/.netrc with your XNAT credentials:

   machine xnat.example.com
    login your-xnat-username
    password your-xnat-password
   

   Option 2: Using .env.local file

   Create a .env.local file in your project directory:

   XNAT_USER=your-xnat-username
   XNAT_PASS=your-xnat-password
   

3. Access to an XNAT server with at least one project.

Basic Example: Running dcm2nifti

This example shows how to convert DICOM files to NIfTI format for a specific subject.

Python API

from pathlib import Path
import xnattools as xt

tools = [xt.Dcm2niftiSettings()]
settings = xt.GeneralSettings(
    system_url="https://xnat.example.com",
    project_id="MY_XNAT_PROJECT",
    subjects=["SUBJECT_001"],
    output_dir=Path.cwd(),
)
xt.run_tools(tools_to_run=tools, general_settings=settings)

Command Line

xnattools dcm2nifti https://xnat.example.com YOUR_PROJECT_ID \
    --subjects SUBJECT_001

Replace YOUR_PROJECT_ID with your actual XNAT project ID and SUBJECT_001 with a valid subject ID from your project.

To use a custom output directory for intermediate files:

Python API

from pathlib import Path
import xnattools as xt

tools = [xt.Dcm2niftiSettings()]
settings = xt.GeneralSettings(
    system_url="https://xnat.example.com",
    project_id="MY_XNAT_PROJECT",
    subjects=["SUBJECT_001"],
    output_dir=Path.cwd(),
)
xt.run_tools(tools_to_run=tools, general_settings=settings)

Command Line

xnattools dcm2nifti https://xnat.example.com YOUR_PROJECT_ID \
    --subjects SUBJECT_001 \
    --output-dir /path/to/temp

Authors

• Martijn P. A. Starmans : m.starmans@erasmusmc.nl
• Erik Kemper : e.h.m.kemper@erasmusmc.nl
• Frederik Hartmann : f.hartmann@erasmusmc.nl