== PCA ==

Unless your dataset is exceptionally large (>400) you will have more dimensions in you dataset than samples. If you need to check, the number of dimensions is twice the number of points in your template (i.e. x and y coordinates in the picture), strictly speaking you can subtract up to 6 as a result of the alignment process but that only works if both you and the stats package understand rank-deficient matrices. In order to reduce that number of dimensions, and reduce the chance of over-fitting we use '''PCA''', fortunately shape PCA is built into Psychomorph in the form of an '''ASM''' (Active Shape Model). 

[wiki:recipes/PCA/explanation PCA (somewhat) explained] - A long winded incoherent rant on the topic.

== The PCA Menu ==
[wiki:recipes/PCA/BuildShapePCA Build Shape PCA (ASM)] – Build an Active Shape Model(ASM) from a set of templates[[BR]]
[wiki:recipes/PCA/BatchAnalyseShape Batch Analyse Shape] – Analyse a set of templates using an ASM and produce a set of PCA parameters[[BR]]
[wiki:recipes/PCA/BatchShapeReconstruct Batch Shape Reconstruct] – Reconstruct a set of templates from a set of PCA parameters using the ASM[[BR]]
---[[BR]]
[wiki:recipes/PCA/BuildImagePCA Build Image PCI] – Build a Principal Components Image (PCI) model from a set of images[[BR]]
[wiki:recipes/PCA/BatchAnalyseImages Batch Analyse Images] – Analyse a set of images uinsg a PCI model and produce a set of PCA parameters[[BR]]
[wiki:recipes/PCA/BatchImageReconstruct Batch Image Reconstruct] – Reconstruct a set images from a PCI model and a set of PCA parameters.[[BR]]
PCA Options[[BR]]
-'''Mask Input Images''' – Mask images prior to bulding PCI model or analysing image sets.[[BR]]
-'''Mask Output Images''' – Mask images reconstructed from PCI model.[[BR]]
-'''Normalise Images''' – Pre-normalise images before building or analysing PCI model.[[BR]]
-'''Save Residual Images'''. – Save residuals from image analysis.[[BR]]


[[Image(average.jpg, width=40)]]