Dear CONN experts,
I am running an MVPA analysis and want to calculate the total variance explained by my components. I understand that the PCAcov file contains the percentage of variance explained by each voxel, and I would like to determine the total variance explained by the components.
The PCAcov files contain a 3D matrix (91×109×91). 242545 voxels have nonzero values, while 660084 are exactly zero. I can compute the mean across all voxels for each component (I know the variance explained is cumulative), but I am unsure whether to:
- Include all values (including zeros) when
computing the mean.
- Exclude zero values, assuming they
represent non-brain or masked voxels.
When I include zeros in the first component, I get a value of 5%, but when I exclude them, the value increases to 17%.
How should I interpret the
zero values in
this context? Does PCA in CONN assign zeros to voxels that do not belong to
any component?
Moreover, is there any chance I could see a mask of the voxels that
contribute to each component?
I appreciate any insights you can provide.
Best regards,
Paula