The XNAT Experiment International Date Format (ISO) Plugin is a modification on velocity scripts to display the fields ‘Experiment Date’ and ‘Date Added’ in the Experiment pages in ISO format, instead of originary MDY date format.
The rationale of that modification is to avoid misinterpretation issues when reading dates in countries not following (nor used to) the MDY data format.
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This plugin is actually a tiny hack for including an additional ‘Display Field’ in mrSessionsData data-type listings with an aggregate of existing resource collections per each MRSession experiment, similar-to and inspired-by the existing mrSessionsData ‘Scans’ field.
The plugin was conceived for easily providing an informative per-session list of resources (i.e. derived data bundles generated from automated processing pipelines).
Important: Note that installing this XNAT plugin implies slightly modifying the database, i.e. creating additional database views.
The XNAT Selectable Table was developed in concert with the Container Service plugin to provide users with a way to run commands on individual scans from an image session report page. However, the selectable table also has UI improvements and convenience functions that can be adopted into XNAT without running Container Services.
Full documentation on using and installing the selectable table plugin is here: https://wiki.xnat.org/documentation/how-to-use-xnat/batching-actions-on-scans-with-the-selectable-table-plugin
The XNAT Container Service plugin allows XNAT to control containers (primarily Docker containers). Containers are a lightweight and flexible way of running processes on XNAT data, similar to pipelines in their usage. Once configured by an XNAT administrator, XNAT users can launch containers on their project data and see results nearly instantaneously.
To use it, you will need an XNAT running 1.7.3+. Get the containers-
A list of XNAT-approved Docker Images that are supported by the Container Service plugin can be found here: https://wiki.xnat.org/display/CS/List+of+Containers+and+Commands
XNAT.osirixplugin has been developed at the Translational Imaging Group (TIG) laboratory at Center for Medical Imaging Computing(CMIC), University College London (UCL), United Kingdom: http://cmictig.cs.ucl.ac.uk/ .
XNAT.osirixplugin is a plugin for OsiriX or Horos developed by Benjamin Yvernault (b.yvernault@ucl.ac.uk). It allows the user to interact with XNAT database directly from OsiriX/Horos interface. You can download DICOM data, upload ROI, and do quality control on your processing. Processing data are stored on XNAT in a specific assessor that is part of DAX python package: https://github.com/VUIIS/dax developed at MASILab, Vanderbilt University, USA. You can read more about the assessor: https://github.com/VUIIS/dax/wiki/DAX-XNAT-Data-types-Installation .
You can download OsiriX from their website: http://www.osirix-viewer.com/ or if you prefer, you can use the free version called Horos: https://www.horosproject.org/ .
You can read more about the plugin on github: https://github.com/byvernault/xnat_osirix_plugin .
The Ribbon plugin allows you to add a display sash to your XNAT 1.6 instance, very similar to the “fork me on github” sashes you sometimes see in other software library homepages. Its main purpose is to indicate testing or staging deployments of XNAT without needing to change any other element of the xnat instance. The uploaded module provides a green “TESTING” sash but you can customise this to your own needs.
Customisation
You can build your own ribbon that customises the following properties:
- text,
- clickable url,
- text color,
- background color,
- border color.
You can do this by cloning the github repository, editing the ribbon-conf.properties file and building your own copy of the module.
XNAT pipeline for forwarding data from local-based XNAT instance to CTP (for anonymisation) and/or to an additional XNAT node.
Using such pipeline eases the eventual anonymisation and export procedure of DICOM data (click and export) and therefore the capability of exchanging specific imaging data sets.
The pipeline consists of the following steps:
(1) Create a directory structure for hosting data
(2) Pulls deflated data from XNAT
(3) Unzip image data
(4) Replace PatientID and PatientName tags with XNAT value for Subject Label by calling DCMTK tools.
(5) Forward data (DICOM C-STORE SCU) to an existing DICOM node
(6) Delete temporary directories & files
(7) Notify (if requested) the end-user when completed.
The following third-party executable apps are used and should be accessible by the pipeline engine:
. dcmodify (DCMTK tool kit)
. storescu (DCMTK tool kit)
Note: This pipeline permits selecting an specific sub-set of scans from a DICOM study to export. If pipeline is called via the REST API without a list of affected scans, all scans are processed by default.
More information on how to install a pipeline in XNAT here: https://wiki.xnat.org/display/XNAT/Installing+Pipelines+in+XNAT
Our add in schema for https://www.brainsimagebank.ac.uk/
The image viewer is an HTML5-based viewer for DICOM and 3D Slicer image data integrated directly into XNAT.
The Visits & Protocols module adds visit scheduling and experiment/session tracking features to XNAT and allows research coordinators greater ability to track project protocol requirements, missed visits and progress reports. This is a beta release candidate currently. Future versions will target the XNAT 1.7 development line and support advanced features like multi-ARM protocols, greater event notification options and protocol report dashboards.
Optical Imaging Session (OIS) data type and processing pipeline. This software was developed for the Joe Culver lab at Washington University for use in the fcMicrobiota project, which uses optical functional connectivity scans to study the effects of immature gut microbiome in mice. This package includes: the OIS data type module, the OIS pipeline module, and a python script for uploading OIS data to XNAT.
The XNATX SchemaDocs module provides an integrated REST-based service to generate documentation from the XNAT data-type schema that are installed in your deployed XNAT application.
This is a version of the XnatDataClient (XDC) tool that ships with the XNAT installation. It has been broken out on its own so that it can be placed anywhere on the user’s system path.
XDC is provided as a Java archive or jar file. The jar file is packaged as a Java application, with the required classpath included in the archive manifest. The practical result of this is that you can run the application just by specifying the XDC jar file (named data-client-version.jar) with the JVM call:
java -jar lib/data-client-1.6.5.jar -h
Once installed, you can run XDC just by typing the script name:
XnatDataClient --version
More information on working with XDC is available on the XNAT wiki: https://wiki.xnat.org/xnat-tools/xnatdataclient
MGA is an multispectral MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis such as multispectral ROI analysis, in both longitudinal and cross-sectional studies. MGA works on DICOM images from a single MRI study. Includes perfusion (DSC sequence based) analysis and DTI analysis, and spatially co-registers all study images to an atlas template and to a template image within the study. MGA is designed to reasonably minimize user configuration steps and to accept a range of MRI submodalities.
XNAT server requirements:
XNAT 1.6.2+
Execution node requirements:
docker.io 1.6+
The process of XNAT pipeline installation is described below.
1. Install the MGA docker virtual appliance from https://bitbucket.org/mmilch01/mga_docker_install
2. Install the latest docker-io Linux package on nodes that will run MGA.
3. Copy java code from xnat_pipeline/src/ to your buildable xnat source
4. Copy pipeline xml from xnat_pipeline/pipeline/ to your XNAT server pipeline repo
5. Rebuild XNAT
6. Install [path to XNAT pipeline catalog]/HOF/HOF.xml pipeline with custom pipeline screen HOFPipelineScreen.vm on your XNAT website in Administer->Pipelines->Add new pipeline.
This script installs a default XNAT service on a Linux Operating System (Ubuntu, Fedora, RedHat, Scientific Linux). The puppet script is based on the XNAT installation manual. Full documentation of this script can be found in the README and INSTALL files on its repository. The README file describes which services are installed and INSTALL how to install the script.
This feature allows users to upload project level resources via the Project Report page. The upload feature is constrained to only allow users to upload to resource names that have been preconfigured by the project owner. The module includes modifications to the Project -> Manage tab to allow OWNERS to specify the resources which can be uploaded to. It also includes modifications to the Project -> Actions box to allow a popup dialog which supports uploading to those resources. Finally, it adds a Resources tab to the project page to display and download project resources.
This module implements a Radiological Assessment datatype, including edit and report pages, to support the “rad read” process. It includes fields such as the reader, technique, findings, and diagnosis.
IQ Assessment Data Type.
A collection of typical clinical data types gathered during patient exams. This package includes:
- Neurological Examination
- Physical Examination
- UA for Pregnancy
- Vitals
“The Uniform Data System (UDS) is a core system of information appropriate for reviewing the operation and performance of health centers. UDS is a reporting requirement for Health Resources and Service Administration (HRSA) grantees, including community health centers, migrant health centers, health care for the homeless grantees, and public housing primary care grantees. The data are used to improve health center performance and operation and to identify trends over time. UDS data are compared with national data to review differences between the U.S population at large and those individuals and families who rely on the health care safety net for primary care.”
Reference: http://www.healthindicators.gov/Resources/DataSources/UDS_161/Profile
Utility that will search for DICOM files on a PACS (via patient Id, patient birthdate, etc) and then send a request (via study instance uid) for the PACS to move the files to a CTP server where they are anonimized / sent to the CNDA.
XNAT DataChooser is a client-side tool for browsing and selecting data from XNAT archives. It is designed to streamline the process of incorporating XNAT functionality into end-user applications and, in its simplest form, operates as a simple one-line drop-in for to replace a standard File -> Open… dialog.
This is the first public release of the application, with the following features:
* flexible user interface for downloading data files from XNAT;
* written entirely in Java, using the Swing GUI toolkit;
* multiple user profiles, to allow flexible login to different
XNAT database, or as different XNAT users;
* flexible searching using a (large) subset of the most useful XNAT
schema entries for image data types;
* creation of virtual directory structure based on search criteria
to allow rapid browing of data;
* download of MRI, CT and PET data already tested;
* flexible framework for adding new XNAT schema datatypes with
associated files for download;
* cache implementation, so that data need to be downloaded only
once;
* full Java API to allow programmatic use of the XNAT DataChooser;
* complete source code included, with comprehensive Java documentation;
* ability to call DataChooser from MATLAB and IDL (full demo of
capabilities provided in distribution) to allow data to be delivered
directly into user applications;
* (next release will feature equivalent functionality to call from
C++ and, if all goes well, Python);
* ability to store table settings for each data type displayed, to
allow customisation of user experience.
Installation should be a piece of cake. Simply copy the file to your home directory, and uncompress it there. Please make sure that the top-level uncompressed directory has name .XNAT_DAO (the dot is important) and resides directly within your home directory. Then take a look at README.txt.
This module contains XML Schema, Velocity templates, JavaScript, and CSS for the data types ExtendedBOLDQC and ManualBOLDQC.
IMPORTANT:
This module requires that you apply a small patch to xnat.xsd before you run update.sh. The patch can be extracted from the module archive:
$ unzip -j mriqc-0.1.zip src/main/patches/xnat.xsd.patch -d /tmp
$ patch ${XNAT_SOURCE}/projects/xnat/src/schemas/xnat/xnat.xsd < /tmp/xnat.xsd.patch
An implementation of the Autism Social Responsiveness Scale (SRS). Includes datatype, display document, report and edit pages. Based on the CNDA implementation.
An implementation of the Autism Diagnostic Observation Schedule (ADOS). Modules 2, 3, and 4. Includes datatype, display document, report and edit pages. Based on the CNDA implementation. 2001 version of the assessment.
An implementation of the Autism Diagnostic Interview-Revised (ADI-R). Includes datatype, display document, report and edit pages. Based on the CNDA implementation. 2007 version of the assessment.
This module adds a calendar restlet to your installation of XNAT that will return an iCalendar feed containing experiments stored within your XNAT. The start time for the experiment event is the start time of the first scan. The end time is the start time of the last scan. If it is a non-imaging session or the start/end time cannot be found it will be listed as an all-day event.
Adding calendar feed to Outlook:
You can add the iCal to Outlook as a web calendar by going to outlook and clicking Calendar > Open Calendar > From Internet. Type in the URL to the restlet with your filters. (e.g. webcal://www.yourxnat.org/data/services/calendar?projects=test1) Outlook will prompt you for your XNAT credentials, then will download the feed and periodically check it for updates. (Outlook will cache this username/password)
Outlook will convert all event times to local time! If your scanner is located in a different time zone, the event time might appear incorrect. Since XNAT does not support time zones there really is no clean fix for this. There are plans to add custom time zone rules to this module. (e.g. admins could set the calendar time zone for a specific project or scanner)
Caveat: I am not sure how this calendar feed will behave in other calendar applications other than Outlook. Since we use Outlook at NRG, that was the main focus.
The calendar feed does contain sensitive information such as project id, subject label, investigator names. Be wary of loading this into web calendar applications such as Google Calendar.
CSV Importer provides a REST interface to import spreadsheet (CSV) data. It is similar to the current Spreadsheet Uploader with better support for data integrity.
The identifying or sensitive anatomical features in MR and CT images used in research raise patient privacy concerns when such data are shared. The Face Masking package implements anatomical surface modification algorithm customized to de-identify MR head images that minimizes the impact on the resulting image statistics.
Face Masking obscures facial features from high-resolution MR scans that need to be shared, to reduce the research subject identification risk. Face Masking is minimally invasive and is designed to run with other processing tools such as skull stripping, MR artifact correction or segmentation.
For instructions on installing this as an XNAT pipeline, see this documentation: http://nrg.wustl.edu/software/face-masking/pipeline/
If you have questions, please contact Misha Milchenko: milchenkom@mir.wustl.edu.
fspet is a package for processing amyloid imaging data (PIB PET) to obtain quantitative information about amyloid load in the brain. Regional quantification is achieved by utilizing FreeSurfer segmentation results (the wmparc.mgz file). The output of this analysis are binding potential and SUVR measurements of cortical gray matter regions, subcortical regions, and white matter regions. Global index of amyloid load is presented as a mean cortical binding potential (MCBP) or an all cortical mean (CALL) measure. The data processing stream requires an input file (see example in the tst folder). The input file specifies the location and name of the PET data (can be both ecat file or dicom file), and the FreeSurfer file (T1.mgz or orig.mgz, and wmparc.mgz). It also asks for the fwhm of the PET data, time range used for quantification.
For additional information contact Yi Su, PhD (suy@mir.wustl.edu)
The 4dfp package is adapted from Avi Snyder’s 4dfp package (avi@npg.wustl.edu)
INSTALLATION
$ cd $FSPET (location of this package)
$ cd 4dfp (enter the 4dfp folder)
$ ./comp4dfp (compile 4dfp package)
$ ./install4dfp (copy 4dfp executables into the bin directory)
$ cd ..
$ cd src (enter the src directory)
$ make ALL
$ cd ..
After these steps, all the binaries should have been generated, the executables are in three locations: 4dfp/bin, scripts, and src. They can be put into user defined executable locations, or these three folders can be added into the path. For installations with existing 4dfp packages, please ignore the 4dfp portion of the installation. The 4dfp folder and the atlas folder can be removed.
After installation the environmental variable FSPET need to be set to run the package.
$ setenv FSPET /location/of/fspet (csh)
$ export FSPET=/location/of/fspet (bash)
TEST
$ cd $FSPET/tst pib_fs_proc bertpib_params.txt
This will generate a pib_proc directory within the tst folder, and perform the analysis there. When the job is done (in a couple of hours), text output will be generated that contains quantification result. Compare the results with the .txt files in the pib_proc_ref directory. The results should be similar.
A simple bash script that takes a directory full of module folders, navigates into each directory and packages the src file as a ZIP, and moves the ZIP into a deployments directory ready for copying into your XNAT 1.6 modules directory.
A Java-based command-line report tool that generates reports about new and modified subjects and experiments. Reports can be either e-mailed to users or generated as local files. Bash and windows batch scripts are provided for convenience in the package.
This module implements an assessor for the NIH Stroke Scale data-type, including edit and report pages. You can find out more about the NIH Stroke Scale at http://www.nihstrokescale.org.