Slicer3: Remote I/O

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Slicer3 Remote I/O Informatics Architecture
for QueryAtlas Other Applications
2008 fBIRN AHM
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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
• Slicers 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

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Prior fBIRN data access in Slicer
Slicers prior data handling approach (lt 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.
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Formats data collections
Slicers prior data handling approach (October
BIRN AHM) permitted loading and saving of local
data only, with capatiblity to handle XCEDE
catalog input.
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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.
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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

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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)

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Architecture details
Includes Cache and Data I/O Managers in MRML
Asynchronous I/O option through Application
Logics queuing and threading mechanisms
Extensible collection of URIHandlers,
including http, srb, xnat
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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.
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XNAT Download Upload
Slicer/XNAT compatibility proceeding in
collaboration with XCEDE Working Group, as a
stepping stone to compatibility with XCEDE web
services
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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.
• Slicers 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 Tuesdays NI WG
  meeting

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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/RemoteTest
  Vtk.mrml - points to Aseg_17_Left-Hippocampus.vtk,
  Aseg_53_Right-Hippocampus.vtk
• http//wiki.na-mic.org/Wiki/images/7/70/RemoteTes
  tMgzVtk.mrml points to the above vtk files as
  well as Aseg.mgz
• http//www.na-mic.org/Wiki/images/e/ec/RemoteTest
  Colours.mrml points to Aseg.mgz and the colour
  file FSColorLabelsTest.ctbl
• http//www.na-mic.org/Wiki/images/3/3d/RemoteTest
  MgzVtkPial.mrml points to Aseg.mgz,
  Aseg_53_Right-Hippocampus.vtk, and lh.pial
• http//www.na-mic.org/Wiki/images/3/37/RemoteTest
  SRBVtk.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/RemoteBe
  rtSurfAndOverlays.mrml points to files on
  http//slicerl.bwh.harvard.edu/data, tests new
  overlay storage nodes.
• http//slicerl.bwh.harvard.edu/data/fBIRN/fBIRN-A
  HM2007.xcat a sample xcat for QueryAtlas demo,
  pointing to files on http//slicerl.bwh.harvard.ed
  u/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-SR
  B.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.