Slicer3:Remote Data Handling

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vtkMRMLStorageNode methods for handling remote data (for loading and saving data for interactive use)

The first goal is to figure out what workflows to support, and a good implementation approach.

Currently, Load Scene, Import Scene, and Add Data options in Slicer all encapsulate two steps:

• locating a dataset, usually accomplished through a file browser, and
• selecting a dataset to initiate loading.

For loading remote datasets, the following options are available:

• break these two steps apart explicitly,
• bind them together under the hood,
• or support both of these paradigms.

Breaking apart "find data" and "load data":

Possible workflow A

• User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
• From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file listed in the archive is downloaded to /tmp directory (always locally cached) by the Download Manager, and then loaded into Slicer via a vtkMRMLStorageNode method when download is complete.

Possible workflow B

• User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
• From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file in the archive is downloaded to /tmp (only if a flag is set) by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete.

Possible workflow C

• User locates a MRML file, .xcat archive, or individual dataset on the HID or an XNAT web interface
• User types the uri into the Load Scene, Import Scene, or Add Data interfaces.
• If no locally cached versions exist, each remote file in the archive is cached to /tmp by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete.

Bundling together "find data" and "load data":

Possible workflow D

In this workflow, Slicer would make calls to HID or XNAT webservices to determine what data of interest is available... Questions:

• How might this work?
• Do we really want to re-implement functionality in the HID web interface?
• Maybe Slicer can implement a workflow (A-C) but also offer a simplified BIRN query interface that has functionality like:
  • Request BIRNIDs for all subjects who have a complete FIPS/FreeSurfer analysis
  • Request an xcat for one of these BIRNIDs

Saving Data back to remote site

• Since we have no plan for where to save MRML files on HID, can we have a webservices function we can call from Slicer that writes a file to /dev/null on HID in the meanwhile?

What data do we need in an .xcat file?

For the fBIRN QueryAtlas use case, we need a combination of FreeSurfer morphology analysis and a FIPS analysis of the same subject. With the combined data in Slicer, we can view activation overlays co-registered to and overlayed onto the high resolution structural MRI using the FIPS analysis, and determine the names of brain regions where activations occur using the co-registered morphology analysis.

The xcede2.0 catalog should contain to associated collections of data for the fBIRN QueryAtlas use case:

   * One FreeSurfer "lh" model and one FreeSurfer "rh" model at most
   * the FreeSurfer structural brain.mgz image volume
   * the FreeSurfer example functional example_func.nii
   * some FIPS-generated Statistical volumes
   * the FreeSurfer aparc+aseg.mgz label map volume
   * the FreeSurfer lh.aparc.annot annotation file
   * the matrix to align the example_func + statistics to the brain.mgz: anat2exf.register.dat 

These are found in the following places, according to the default FIPS/FreeSurfer directory structure.

The BIRN HID webservices shouldn't really need to know the subset of data that QueryAtlas needs... maybe the web interface can take a BIRN ID and create a FIPS/FreeSurfer xcede catalog with all FIPS/FreeSurfer uris, and Slicer can parse out the ones of interest, and download them?

See this page for more discussion of Slicer's use of Xcede catalogs