Created
July 24, 2017 13:12
-
-
Save jvsoest/6136be82801b0cfa159925f2f4259e1a to your computer and use it in GitHub Desktop.
XNAT python
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ###### login to XNAT and search/get files ######## | |
| import xnat | |
| session = xnat.connect('https://xnat.bmia.nl', user='bla') | |
| session.projects | |
| project = session.projects['STW_STRATEGY_HN_VELLORE'] | |
| subject = project.subjects['BMIAXNAT_S08453'] | |
| experiment = subject.experiments['BMIAXNAT_E28844'] | |
| scan = experiment.scans['701'] | |
| #download the actual scan (which means zip at XNAT, download zip file) | |
| scan.download('~/701.zip') | |
| ####### unzip ####### | |
| import zipfile | |
| import os | |
| zip_ref = zipfile.ZipFile('~/701.zip', 'r') | |
| os.mkdir('~/701') | |
| zip_ref.extractall('~/701/') | |
| zip_ref.close() | |
| ####### read dicom ###### | |
| import dicom | |
| dFile = dicom.read_file('~/701/test1234_20170608_/scans/701-unknown/resources/DICOM/files/1.3.6.1.4.1.40744.29.171823746954830055731259734691543906281-701-10-sktbhh.dcm') | |
| dFile.PatientName | |
| dFile.PatientID | |
| dFile.StudyDate | |
| dFile.SeriesDate | |
| dFile.Modality |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment