Difference between revisions of "Projects:ARRA:SlicerEM:AtlasCreator:PCA"
From NAMIC Wiki
| Line 125: | Line 125: | ||
-va (first) (Optional) define a file name to which results should be written | -va (first) (Optional) define a file name to which results should be written | ||
| + | |||
| + | </pre> | ||
| + | |||
| + | === Representation functionality === | ||
| + | <pre> | ||
| + | $ pcaModelling -HELP representation | ||
| + | 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 | ||
| + | |||
| + | representation = Determines the shape representation from the PCA shape parameters | ||
| + | To turn shape parameters into shape representation (the opposite of function parameter) | ||
| + | -list = the <STRUCTURE> to be considered, e.g. Background | ||
| + | -path = the path of the location of the PCA directory | ||
| + | where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage | ||
| + | e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground | ||
| + | -max = the maximum number of Eigenvectors to considere | ||
| + | -va (first) = the list of shape parameters, e.g. (1.0 3.4) | ||
| + | -va (second) = directory, where the resulting shape representation should be saved to | ||
| + | -combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I) | ||
| + | |||
| + | |||
| + | </pre> | ||
| + | |||
| + | === View functionality === | ||
| + | <pre> | ||
| + | $ pcaModelling -HELP view | ||
| + | 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 | ||
| + | |||
| + | To turn the shape representation into shape parameters | ||
| + | -list defines the <STRUCTURE> to be considered, e.g. Background | ||
| + | -path defines the path of the location of the PCA directory | ||
| + | where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage | ||
| + | e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground | ||
| + | -max defines the maximum number of Eigenvectors to considere | ||
| + | -combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I) | ||
</pre> | </pre> | ||
Revision as of 20:38, 10 March 2011
Home < Projects:ARRA:SlicerEM:AtlasCreator:PCAContents
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
Main
$ 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 =======================
Distance functionality
$ pcaModelling -HELP distance
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
To transfere the labelmap into a distance map according to the PCA model please define the following values:
-path = where should the file be save to
-volume = defines the labelmap
-va (first) = defines the label of interest
-va (second) = Maximum value in the distance map in Euclidean norm (e.g. 100)
-va (third) = Distance value of boundary (e.g. 10)
Generate functionality
$ pcaModelling -HELP generate
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
To generate the PCA the training data has to be organized the following way
<PATH>/case*/<STRUCTURES>/I
where
-path defines <PATH>
the different subjects have to be named case<No>
-list defines the different <STRUCTURES>
e.g. /projects/iccv05/TestExample/TestEMPCASeg/PCATraining/distance/case1/Background/I.*
with -path = /projects/iccv05/TestExample/TestEMPCASeg/PCATraining/distance and -list (Background Foreground)
In addition:
-max defines the maximum number of Eigenvectors to compute
-full defines the full image range, e.g. 1 124, where PCA might only be computed for 40 90
The results will be located in <PATH>/PCA<STRUCTURES>
-combine = define all structures in one PCA model (= 1) or define a PCA model for each structure independently (=0)
-va do you want to normalize the mean distance map so that it is a real distance map (generally a bad idea)
Model functionality
$ pcaModelling -HELP model
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
To turn the shape representation into 3D models
-list defines the <STRUCTURE> to be considered, e.g. Background
-path defines the path of the location of the PCA directory
where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage
e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground
-max defines the maximum number of Eigenvectors to considere
-combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I)
Parameter functionality
$ pcaModelling -HELP parameter
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
To turn the shape representation into shape parameters
-list defines the <STRUCTURE> to be considered, e.g. Background
-path defines the path of the location of the PCA directory
where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage
e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground
-max defines the maximum number of Eigenvectors to considere
-volume defines the volume that should be transfered from a shape representation into PCA parameters
-combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I)
-va (first) (Optional) define a file name to which results should be written
Representation functionality
$ pcaModelling -HELP representation
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
representation = Determines the shape representation from the PCA shape parameters
To turn shape parameters into shape representation (the opposite of function parameter)
-list = the <STRUCTURE> to be considered, e.g. Background
-path = the path of the location of the PCA directory
where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage
e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground
-max = the maximum number of Eigenvectors to considere
-va (first) = the list of shape parameters, e.g. (1.0 3.4)
-va (second) = directory, where the resulting shape representation should be saved to
-combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I)
View functionality
$ pcaModelling -HELP view
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
To turn the shape representation into shape parameters
-list defines the <STRUCTURE> to be considered, e.g. Background
-path defines the path of the location of the PCA directory
where the subdirectory of PCA<STRUCTURE> define EigenValues_<STRUCTURE>.txt, EigenVector*, and MeanImage
e.g. -path is /projects/iccv05/TestExample/TestEMPCASeg and all necessary files are located in /projects/iccv05/TestExample/TestEMPCASeg/PCABackground
-max defines the maximum number of Eigenvectors to considere
-combine just set this parameter if you have one PCA model for multiple structures bc the directory structure is sliglhty different (e.g. TestEMPCASegBlub/PCATraining/distance/PCAFore_Back/Background/EigenVector5/I)
