Difference between revisions of "AHM2009:Batchmake and XNAT"
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(New page: Back to AHM_2009 Breakout session Moderator: Julien Jomier, Dan Marcus Agenda:) |
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Back to [[AHM_2009]] | Back to [[AHM_2009]] | ||
− | Breakout session Moderator: Julien Jomier | + | Breakout session Moderator: Dan Marcus |
+ | (Julien Jomier will not be attending the meeting) | ||
Agenda: | 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. |
Latest revision as of 05:24, 6 January 2009
Home < AHM2009:Batchmake and XNATBack to AHM_2009
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.