Setup

Here you can find help with the setup of Jupyter Notebook and access data on server using Pyxnat.

Table of contents

Setup
1. Access the data on XNAT with pyxnat

Access the data on XNAT with pyxnat

Pyxnat library provides a nice API interface to access data on XNAT.

The data is organized hierarchically:

Project └── Subject └── Experiment └── Scan └── Resource └── File

Setup the connection

Create a configuration file

On terminal connected to the remote server:

  cd
  echo '{"server": "http://10.0.3.12", "user": "<user>", "password": "<password>"}' >> xnat_config.cfg

Connect to a project

  import pyxnat
  interface = pyxnat.Interface(config='<path to config file>')
  project = interface.select.project('<project name>')

Check the connection
```
  print(project.exists())
  >>> True
```

Projects

List all available projects on XNAT

for project in interface.select.projects():
  print(project.label())

Select a project and check if it exists (project is singular here and plural in the previus example)
```
project = interface.select.project('<project label>')
print(project.exists())
>>> True
```

Subjects

List all the subjects in a project

  for subject in project.subjects():
      print(subject.label())

Select one

  subject = project.subject('<subject label>')
  print(subject.exists())
  >>> True

Sessions

Each subject can have multiple sessions (e.g. before-after). In pyxnat they are called experiment

  for session in subject.experiments():
      print(session.label())

  session = subject.experiment('<session label>')
  print(session.exists())
  >>> True

Scans

List the scan ids (numbers) and descriptions

  for scan in session.scans():
      print(scan.label(), scan.attrs.mget({'type'})[0])
  >>> 1 Localizer
  >>> 2 MPRAGE
  >>> ...

Select a scan (should use scan label: number as a string)

  scan = session.scan('<scan label>')
  print(scan.exists())
  >>> True

Resources

Resource can be a different file format (e.g. DICOM or NIFTI)

  for resource in scan.resources():
      print(resource.label())

  resource = scan.resource('<resource label>')
  print(resource.exists())
  >>> True

Files

A resource can have multiple files (e.g. separate file after each processing step)
```
  for file in resource.files():
      print(file.label())
```

Access the full path of a file stored on XNAT

  file = resource.file('<file label>')
  print(file.exists())
  >>> True

  print(file._uri)
  >>> '/data/projects/<project label>/subjects/<subject label>/experiments/<session label>/scans/<scan label>/resources/<resource label>/files/<file label>'

Download data

Call .get() function on a Resource or File object. For example, to download all files in a resource:

  resource = project.subject('<subject id>').experiment('<session id>').scan('<scan id>').resource('<resource id>')
  resource.get('<local directory path>') # this is where the files (in a zip archive) will be downloaded to

Upload data

Similarly, can call .insert() funciton on Resource or File. E.g. to upload a file to a resource:

  file = resource.file('<remote filename>') # this is the name the file will appear on XNAT
  file.insert('<local file path>') # this is the path to the file stored locally

Check that the file exists on XNAT:

  print(file.exists(), file._uri)
  >>> True remote/file/path

Delete data

Delete a file or a resource

  file.delete()
  print(file.exists())
  >>> False

Simple processing example

Go through each subject in a test project, download files from nifti resource for mprage scans, extract the brains using fsl bet command and upload the result back to the nifti resource

  import pyxnat
  import os

  interface = pyxnat.Interface(config='/home/roman/xnat_config.cfg')
  project = interface.project('test')

  for subject in project.subjects():
      for session in subject.experiments():
          for scan in session.scans():

              if scan.attrs.mget({'type'})[0] == 'mprage':

                  resource = scan.resource('nifti')
                  file = resource.file('mprage.nii.gz')
                  assert file.exists(), 'Mprage file does not exist for subject {}'.format(subject.label())

                  # Download the file
                  t1_filename = file.get('/home/roman/Downloads')

                  # Extract the brain
                  t1_filename = t1_filename.replace('.nii.gz', '') # remove the extension
                  brain_filename = t1_filename + '_brain'
                  ! bet {t1_filename} {brain_filename}

                  # Uplaod the file
                  remote_name = os.path.basename(brain_filename) + '.nii.gz'
                  local_name = brain_filename + '.nii.gz'
                  resource.file(remote_name).insert(local_name)

                  # Check that the upload worked
                  assert resource.file(remote_name).exists(), 'Upload did not work for subject {}'.format(subject)