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TODO

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critical

  • integrate registration methods.
  • add roi viewing/editing to gui (viewing done)
  • add conditions to info server
  • fix incremental GLM (DONE)
  • look into image saving (DONE)

config:

  • allow spec of input data ids in module names

logging:

  • adapt ace logger framework to allow writing to files and screen simultaneously.
  • provide nice interface for logging
  • add auto logging code to processing

streams:

  • work on serial/parallel processing dependencies
  • allow easier accessing of data produced earlier in a stream
  • consider eliminating distinction between preprocessing, analysis, and postprocessing

data

  • enforce directory structure (make structure as well)
  • make standardized interface to serialize data using XML.
  • clean up setInfo parts of RtActivation and RtMaskImage (for creation based on geometry of other images)
  • add interator type interface for mask image
  • convert to nii image representation
  • convert all numerics to vxl
  • enforce data persistence accounting
  • make sure all non-persistent data cleaned up after stream completion
  • develop flexible, efficient method for retreiving persistent data (hashing?). make available to gui and info server as well
  • also develop either method for unique ids for each data instance or iterator method to choose like data
  • think about id stuff (make id strings consistent ‘-‘,’_’, etc.)
  • add nifti reading/writing (DONE)
  • add (un)mosaic

data structures

  • fill out functionality in RtDataImage.h and turn it into a .txx
  • roi
  • RtMaskImage has duplicated functionality to handle RtMRIImage and RtActivation

algorithms

  • cox (1995) accumulative correlation (DONE, but sux)
  • indiv voxel least squares solver (DONE, but adapt to voxel unspecific calcs)
  • gembris (2000) sliding window correlation
  • kalman filter (rouche 2004)
  • hinds (2008) single image correlation first implementation done. method needs to be extended to allow arbitrary contrasts
  • add baseline scans at beginning to let stabilize (DONE)
  • roi activation (DONE)
  • roi-based spatial subtraction (DONE)
  • completely general ROI sum arithmetic
  • hooks for external apps
    • motion correction
    • intensity normalization
    • registration
    • brain mask computation (DONE)

communication

  • fix Nan problem
  • setting up stim schedule
  • add conditions to infoserver

simple gui

  • overlay (z-scores on epi) (DONE, but need fixed)