Downloading NIfTI resources from XNAT

November 02, 2018

It is quite common that we use XNAT to download a bunch of NIfTIs to run some external analysis.

This generic example shows how to download NIfTI resources from an XNAT instance. In this context, NIFTI resources are stored at the scan level (subject/experiment/scan).

In this example, for every subject of a given list subjects, we need to download two sequences (their SeriesType being DWI_ALFA1 and rDWI_ALFA1 but may be anything else).

Note: We will be using the pyxnat library to make REST API calls from Python code.

config_file = '/home/grg/git/bbrc-validator/.xnat.cfg'
dest_dir = '/tmp/'
subjects = ['SUBJ_003']
project = 'testenv'
scantypes = {'DWI': ['DWI_ALFA1'],
             'rDWI': ['rDWI_ALFA1']}

import logging as log
from pyxnat import Interface
import os.path as op
log.getLogger().setLevel(log.INFO)
log.info('* configuration file: %s'%config_file)

c = Interface(config=config_file)
experiments_id = {}
subjects_id = {}

# Fetching subjects from project
subjects_pr = c.select.project(project).subjects()
subjects_id = [e for e in subjects_pr if e.label() in subjects]

for subject in subjects_id:
    log.info('Project: %s Subject: %s'%(project, subject.label()))

    # For each subject we assume there is one MRsession only
    exp = c.array.experiments(project_id=project, subject_id=subject.id()).data
    exp_id = exp[0]['ID']

    # Fetching scans
    scans = c.array.scans(experiment_id=exp_id,
      columns=['xnat:mrscandata/type']).data
    for m, st in scantypes.items():
        items = [sc['xnat:mrscandata/id'] for sc in scans \
                 if sc['xnat:mrscandata/type'] in st]
        log.info('Type %s: %s'%(m, items))
        if len(items) == 1:
             # Building the NIFTI resource URL
             res = [e for e in c.select.experiment(exp_id).scan(items[0]).resources()\
                if e.label() == 'NIFTI']

             # Downloading it             
             log.info('* Downloading %s in %s...(%s)'\
              %(subject.label(), op.join(dest_dir, e.id()), m))
             res = res[0].get(dest_dir)

        else:
            log.info('Found duplicates. %s'%items)

Many thanks to Jordi Huguet from BarcelonaBeta for his valuable and continuous help with this matter.

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