Slicer3:XCEDE use cases

Slicer3 use cases for XCEDE

Query Atlas Module

This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:

• 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

Assumptions:

• we are assuming a single lh or rh model (or one of each) is in the catalog. (Reason: Slicer will load the lh.aparc.annot file as a scalar overlay onto a model; so the overlay needs to be associated with a model automatically during load. Since the catalog attribute list contains no references to other datasets, the only way to associate the lh.aparc.annot to the lh.pial surface is by matching on the "lh." and "rh." in the model and annotation names.)

• we are detecting whether a matrix with the name "anat2efx" is in the catalog (we should probably check the uri instead) -- and if so, we are wrapping the list of all FreeSurfer volumes and models (noted above) in a derived transform in the load routine.

New value inventions for attributes:

• Freesurfer:matrix-1 (this gives us a clue about file format).
• Freesurfer:overlay-1 (for files that need to be associated with a model in order to load in Slicer)
• Freesurfer:label-1 (for mgz files that are label maps) This gives us a hint about what kind of color map to use to display the image data. The default colormap for volume data is greyscale.

Current Xcede catalog importer notes and to-do:

• We recognize files with the string "brain.mgz" "example_func" and "stat" in them, in order to do some aautomatic calculation of the Slicer transform that does the ras2ras registration intended by the FreeSurfer matrix anat2exf.register.dat.
  • the tests to detect these files are weak -- need a better test: now, a structural volume with the string 'stat' embedded in it will be stuffed into the transform by mistake.
  • no registration transform will be computed if volumes matching the brain.mgz, example_func and an anat2exf.register.dat file are not detected.
  • a transform will be computed using the brain.mgz and example_func volumes and the anat2exf.register.dat

• Something inside the tcl proc that reads the anat2efx is causing vtkDebug leaks. find and fix.