mattsouth

import pyxnat
import os
import time

# A python 2.7 / pyxnat script for downloading the resources from an xnat project

# gather source xnat details
print '** DOWNLOAD XNAT PROJECT RESOURCES **'
xnat_url=raw_input("Enter the xnat url: ")
project_name=raw_input("Enter the xnat project id: ")

mattsouth

#!/bin/bash

# bash script to remove unwanted files in xnat using the XnatDataClient
# iterates through all sessions looking for particular scan types with particular file types and file name patterns

# CLI parameters:
# 1. url - xnat url
# 2. username - xnat username
# 3. project - xnat project
# 4. scan type - e.g. "STRUCTURAL", "FLAIR"

mattsouth

#!/bin/bash
# creates subject / experiment ids if they dont already exist
# 1. url - xnat url
# 2. session - tomcat session_id (instead of username / password)
# 3. project - project id
# 4. subject - subject_id
# 5. experiment - experiment id
# 6. date - experiment_date
# 7. verbosity - 0 = surpress, 1 = log (default), 2 = debug

mattsouth

class exports.Ticker
  constructor: (timeout) ->
    @timeout = timeout || 1000

  _nextTick: =>
    @tick = setTimeout(@_nextTick, @timeout)
    console.log 'tick'

  start: ->
    @_nextTick()

mattsouth

# Renames every MR experiment, thus kicking off the anonymisation script.
# see https://groups.google.com/d/msg/xnat_discussion/vvLyLvyo2uQ/yMPHgkrOEwAJ
# used in XNAT 1.6.5
# also see https://groups.google.com/d/msg/xnat_discussion/fBI33j36D3Y/VEwh-HWez70J for discussion about changing experiment label
import xnat # see https://xnat.readthedocs.io/en/latest/

url = raw_input("Enter XNAT url: ")
user = raw_input("Enter username: ")
with xnat.connect(url, user=user) as session:
    name = raw_input("Enter project: ")

mattsouth

# outputs a summary of the data in an xnat project, e.g.:

# 55 subjects, 65 scans, 400 sequences (SNAPSHOTS: 400, DICOM: 400, NIFTI: 200)

# Note that in our lab we talk about "scans" and "sequences" which correspond
# to xnat's "MR Sessions" and "Scans" respectively.

# Parameters:
# 1. url - xnat url
# 2. username - xnat username

mattsouth

# prints the subject_id and experiment_id of XNAT experiments where a scan is missing a snapshot
# used against XNAT 1.6.5 by python 2.7
import xnat # see https://xnat.readthedocs.io/en/latest/

url = raw_input("Enter XNAT url: ")
user = raw_input("Enter username: ")
session = xnat.connect(url, user=user)
name = raw_input("Enter project: ")
project = session.projects[name]

mattsouth

# prints the subject_id and experiment_id of XNAT experiments whose scans are all missing snapshots 
# used against XNAT 1.6.5 by python 2.7
import xnat # see https://xnat.readthedocs.io/en/latest/

url = raw_input("Enter XNAT url: ")
user = raw_input("Enter username: ")
session = xnat.connect(url, user=user)
name = raw_input("Enter project: ")
project = session.projects[name]

mattsouth

#!/bin/bash
# upload pre-processed niftii images to xnat 1.6.5
# 1. xnat - xnat url, e.g. https://central.xnat.org
# 2. username - xnat username
# 3. password - xnat password
# 4. project - project id
# 5. subject - subject id
# 6. session - session id
# 7. scan - scan id
# 8. nifti - filepath of nifti image

mattsouth

import pyxnat
import os
import shutil
import requests
import zipfile
import requests
import time

# A python 2.7 / pyxnat script for copying an xnat project which consists of
# subjects with multiple MRSession experiments