Some important notes on smoothness estimation
The R-package (from version 0.1.1) is able to compute the smoothness parameters of the underlying Gaussian Random Field model based on the 4D residual file, which is more accurate than Z-stat image based smoothness. This is the recommended way to assess image smoothness.
NOTE: the current implementation of the 4D residual-based smoothness estimation is not optimal and can be slow. Please consider using the FSL smoothest command line program and pass its outputs "VOLUME" to the "volume" parameter and "VOLUME"/"RESELS" to the
The 4D residual file can be obtained:
- FSL: <feat_analysis_folder>/<cope.X.feat>/stats/res4d.nii.gz Alternatively you can use the smoothness information written out by feat into the text file called "smoothness" (in the same directory) and pass the necessary values to pTFCE as above (make sure to compute the number of resets as "VOLUME"/"RESELS")
- AFNI 3dLME: Use the "-resid PREFIX" to output the 4d residual file.
- SPM: See this link.
Or use the values from SPM.mat to rely on the SPM-like smoothness estimation:
- search volume: SPM.xVol.S
- number of resels: SPM.xVol.R(4) Note that the pTFCE SPM Toolbox uses the values from the SPM.mat.
