Projects:ARRA:SlicerEM:AtlasCreator:PCA

PCA functionality for the Atlas Creator

This content describes the PCA functionality of KilisSandbox.

Create environment for pcaModelling on Mac

$ tcsh
% cd /Users/daniel/SLICER/TRUNK/Slicer3/Modules/KilisSandbox/scripts
% source setEnvironment
% /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch xterm

pcaModelling Help

$ pcaModelling

Slicer home is /Users/daniel/SLICER/TRUNK/Slicer3-build
============================ Start PCADistance =======================
Always look at vtkEMPrivateSegment/projects/iccv05/TestExample to see example structure
Now can read in raw data with extension .img
load multiple volumes by doing -pr "<dir>/*/prefix" eg case*/I.001 - 001 is important bc file has to exist
=============================
General Options
-ld = load data - default: "1"
-pr = file prefix (mandatory)
-p2 = file prefix of second Volume
-sv = saving output in file formate (sli, img, hdr (analyze), nhdr or nrrd (NRRD),
                              mhd or mha (Meta), nii (Nifti), vtk) - default: nrrd
-va = value for function, default: 0.0
=============================
-fc = function (mandatory) - possibilities:
   distance       = Turns a labelmap into a distance map as needed for PCA modelling (*)
   generate       = Generate the PCA model from the training data (*)
   model          = Turns PCA analysis into 3D models (*)
   parameter      = Extracts the PCA shape parameters from a shape representation (e.g. distance map) (*)
   representation = Determines the shape representation from the PCA shape parameters (*)
   view           = View the PCA model (*)

-HELP = help function If the description of a function has (*) then execute -HELP <function> for more detail, e.g. mathImage -HELP com

Error: Currently function "" is not implemented
============================ End MathImage =======================