AHM2009:Batchmake and XNAT

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

Agenda:

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 ${xnatData})
   echo(${xnatFilename})
   # Get the URI of the datasets
   GetXnatURI(xnatURI ${xnatData})
   echo(${xnatURI})
   # Download the datasets
   DownloadXnatDataSet(${xnatData} 'C:/Julien/TestXNAT')
 EndForEach(${xnatData})

• 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.