Slicer3: Remote I/O & Informatics Architecture for

QueryAtlas & Other Applications

2008 fBIRN AHM

Overview & motivation

Motivation: QueryAtlas requires deeper informatics infrastructure within Slicer in order to query and transact with BIRN data repository and other informatics resources.

Overview:

• Slicer’s prior fBIRN data handling approach

• Target data handling implementation

• Approach

• Status & to-do

• Architecture

• GUI

• Current XNAT interaction (toward interaction with XCEDE web services

• Current limitations

Prior fBIRN data access in Slicer

Slicer’s prior data handling approach (<= october BIRN AHM) permitted loading and saving of local data only.

All datasets were downloaded(or uploaded) externally to Slicer, and loaded into the application from local disk.

Formats & data collections

Slicer’s prior data handling approach (October BIRN AHM) permitted loading and saving of local data only, with capatiblity to handle XCEDE catalog input.

Loadable data:

• XCEDE catalogs• XNAT catalogs• MRML files• individual datasets

Target remote data handling

We want our target implementation to work with XCEDE and other web services client tools to query and transact with BIRN and other data repositories, and support standard data formats and descriptions.

Approach

For Slicer/QueryAtlas programmatic data query and download of fBIRN data are goal. Going through a web GUI where required is reasonable.

Data QueryAtlas requires for fBIRN use case:

• Anatomical scan (anatomical context)• FIPS statistics ( analysis results)• FreeSurfer morphology analysis (for atlas-based info linked to ontology)

Status: Upload and mark-up of these BIRN resources is underway, but not yet complete.

Approach: We are building informatics infrastructure in Slicer, in collaboration with the XCEDE working group to make Slicer XCEDE compatible while data is being described & published. QueryAtlas will leverage this infrastructure to transact with other DBs also

Current implementation status:

• Transact with any remote store using http/curl• Transact with SRB using S-commands• Parse XNAT catalogs (.xcat) & download remote references• Upload datasets to XNAT using xnat-tools (ArcPut)

Architecture details…

Extensible collection ofURIHandlers, includinghttp, srb, xnat…

Asynchronous I/O option through Application Logic’s queuing and threading mechanisms…

Includes Cache and Data I/O Managers in MRML

Preferences and feedback via GUI

Application registry settings for cache and data I/O preferences

Cache and data I/O manager GUI, provides feedback and control.

XNAT Download & Upload

Slicer/XNAT compatibility proceeding in collaboration with XCEDE Working Group, as a stepping stone to compatibility with XCEDE web services

Current limitations

•Lack of standard data descriptions (for label maps, statistical volumes, FreeSurfer models, statistics, and matrices, etc.) Without descriptions, Slicer makes use of filenames and extensions in some cases in order to know how to load datasets.

•Slicer’s data model currently causes problems loading some types of data asynchronously; curl conflicts can arise during asynchronous downloading catalog data containing remote references to matrices for instance…

•Ability to cancel data transfers not yet implemented

•Adding unique tags and identifiers onto XNAT uploads not yet implemented

•Need standard description for data provenance.

• Implementation, including mechanisms for query, is still developing.

• Use cases for discussion at Tuesday’s NI WG meeting

Test data: mrml scene files and xcats

• http://www.na-mic.org/Wiki/images/7/7b/RemoteTest.mrml - points to CTHeadAxial.nrrd

•http://wiki.na-mic.org/Wiki/images/c/cd/RemoteTestVtk.mrml - points to Aseg_17_Left-Hippocampus.vtk, Aseg_53_Right-Hippocampus.vtk

• http://wiki.na-mic.org/Wiki/images/7/70/RemoteTestMgzVtk.mrml points to the above vtk files as well as Aseg.mgz

• http://www.na-mic.org/Wiki/images/e/ec/RemoteTestColours.mrml points to Aseg.mgz and the colour file FSColorLabelsTest.ctbl

• http://www.na-mic.org/Wiki/images/3/3d/RemoteTestMgzVtkPial.mrml points to Aseg.mgz, Aseg_53_Right-Hippocampus.vtk, and lh.pial

• http://www.na-mic.org/Wiki/images/3/37/RemoteTestSRBVtk.mrml points to a file on the BIRN SRB /home/naucoin.harvard-bwh/aseg_17_left-hippocampus.vtk (for now, requires that the uri string start with srb://) SRB clients must be installed first.

• http://slicerl.bwh.harvard.edu/data/bert/RemoteBertSurfAndOverlays.mrml points to files on http://slicerl.bwh.harvard.edu/data, tests new overlay storage nodes.

• http://slicerl.bwh.harvard.edu/data/fBIRN/fBIRN-AHM2007.xcat a sample xcat for QueryAtlas demo, pointing to files on http://slicerl.bwh.harvard.edu/data/fBIRN (manually download the xcat; its references are loaded remotely)

• http://slicerl.bwh.harvard.edu/data/fBIRN/BIRN-QA-XNAT.xcat a sample xcat file pointing to files on host http://central.xnat.org (manually download the xcat; its references are loaded remotely) XNAT tools must be installed first and included in path.

•http://wiki.na-mic.org/Wiki/images/a/ac/BIRN-QA-SRB.xcat points to files on the BIRN SRB /home/Public/FIPS-FreeSurfer-XCAT (manually download the xcat; its references are loaded remotely) For now, requires that the uri string start with srb:// SRB clients must be installed first.