Hi all,
I'm interested in running AlphaSim to calculate minimum cluster sizes
for ROIs within my SPM analyses to reach a corrected significance
level of p < .05. For example, I have the results of a group analysis
and would like to have cluster thresholds for my regions of interest
(dPFC, amygdala). A few questions for those who use AlphaSim:
When calculating FWHM (using 3dFWHMx):
- What is the dataset (i.e. -input or -dset)? That is, what does it
represent and how do I get it from my SPM results?
- If I'm interested in minimum cluster size for a particular ROI,
should I calculate FWHM specifically for that ROI, or whole-brain?
- Should the mask be anatomically-based (i.e. binary) or
functionally-based (with significance values for each voxel)? Again,
how would I get this in SPM?
- Is 3dcopy an ok way to convert the dataset/mask from Analyze to AFNI format?
- Do I need any parameters other than -dset and -mask?
When running AlphaSim:
- Can/should the same ROI mask that was used for calculating FWHM be
used to threshold the AlphaSim analysis?
- Given that when using a mask AlphaSim takes the dimensions and voxel
sizes from the mask, is any consideration given to the native space
dimensions/voxel sizes?
I have AFNI up and running; I just want to make sure I'm using the
proper inputs.
Thanks!
Patrick
|