Slicer3:XNAT

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Background

Existing Slicer3 Interface

Illustration of download process

Basic steps:

  • Browse to the desired image data set
  • Select Download Images
  • Pick which images you want
  • Select the filetype as "xar (3D Slicer)"
  • When the browser asks what to do with the file, select Slicer3 as the application (browse to where the program is installed).
  • Once downloaded, Slicer will look in the file and offer to load the images.

Planned improvements:

  • Fundamental goals for this project:
    • is to be able to upload raw data into the database (core xnat feature)
    • download selected datasets to slicer (see above)
    • run analysis routines in slicer
    • upload the results linked back to original data
  • Further nice-to-have goals:
    • use XNAT as an optional back end for the integration of BatchMake for population processing and parameter space exploration
    • upload analysis results (numerical values) to database for plotting and other analysis

Installation

Options:

  • use the xnat installer script from Gabriele Fariello (fariello at fas.harvard.edu)
    • this works for some linux distributions (Red Hat and probably Ubuntu)
    • you must have Sun Java installed (not the gnu version)
    • best to use this installer on a fresh machine
    • apt-get of postgres may hang waiting for you to press 'Y'

Tests

Get the xnat webservices command line tools from http://www.xnat.org/tools.html#


ArcGet -host www.oasis-brains.org -u guest -p guest -s OAS1_0001_MR1

Further XCEDE Integration

Slicer3:XCEDE_use_cases

Simple tutorial: using XNAT Desktop to upload data

Slicer3:XND

User Requests

Potential users of this project, please list feature requests and/or proposed use scenarios in this section.

  • How is patient deidentification handled in XNAT?