AHM2009:Batchmake and XNAT

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Back to AHM_2009

Breakout session Moderator: Dan Marcus (Julien Jomier will not be attending the meeting)


Accessing XNAT from BatchMake

  • Current status
    • Several commands have been added to BatchMake to support catalog (xcat) parsing from XNAT.
    • Commands have been added to download datasets (using cURL) from XNAT
    • The following script loops through the datasets in an XNAT catalog and download each datasets. Once the dataset is loaded subsequent processing can be performed
 # Set the XNAT catalog downloaded from XNAT Central
 Set(xnatCatalog 'C:/Julien/NeuroMRT_10_MR_1_12_23_2008_12_54_56.xcat')
 echo ('Xnat Tests')
 # Parse the catalog and return a list of URI/Names
 GetXnatDataSets(xnatDatas ${xnatCatalog})
 # Loop through all the datasets in the catalog
 ForEach(xnatData ${xnatDatas})
   # Get the filename of each datasets
   GetXnatFilename(xnatFilename ${xnatData})
   # Get the URI of the datasets
   GetXnatURI(xnatURI ${xnatData})
   # Download the datasets
   DownloadXnatDataSet(${xnatData} 'C:/Julien/TestXNAT')
  • In progress
    • Support for other XNAT installations not tied to central.xnat.org
    • Adding command for uploading files back to XNAT (REST API was not working at the time)
  • Other BatchMake progress
    • Support for Condor has been improved
    • Several new commands have been requested and have been implemented to facilitate data browsing
  • Todo
    • Ron suggested that BatchMake produces a MRML file corresponding to the result of the processing so that it can be loaded into Slicer. I'm not sure how easy it would be and having a use case would be helpful.