AlphaSim in Rest fMRI

I performed an fMRI task for attention. Then using the 'con files' of all the subjects, I performed a multiple regression analysis in SPM8, with a behavioral score as covariate to identify the regions that have a positive or negative correlation with the score. I want to perform AlphaSim for this multiple regression analysis to find the minimum cluster size for alpha 0.05. My uncorrected p value is 0.01, slice thickness is 3 mm.
What should I input for the mask image? Can I use the 'mask' image generated during the regression analysis?
What is the cluster distance? Is it the same as slice thickness?
How to calculate the FWHM for the data? I performed the smoothing at 6mm FWHM.
Thanks and regards,

Shilpi Modi,
NMR research Centre,

1. Yeah, use that mask is fine.
2. If you voxel size is 3x3x3, then use rmm=5 is fine, this means edge connected for cluster. (4 for face connected, and 6 for corner connected)
3. You can use FSL, AFNI or my matlab program y_Smoothest ( to estimate the smoothness (y_Smoothest will be integrated into the next release of REST).

Thanks for publishing that script. I have a question related to that:
I wonder if one should rather use the residuals of the GLM, i.e. the file ResMS.img or if it is better to use the con image (e.g. con_0004.img) or even the spmT (e.g. spmT_0004.img) images to determine the inherent smoothness? What would you propose?

I calculated the values with your program and then read that SPM itself does calculate FWHM during the results process. The values are given on the results sheet of SPM in the Graphics window on the bottom. However these values and the ones I got with your method (irrespective of the image I used, see above) differ in a way. Do you know what you do differently than SPM? I think SPM takes the residuals as described by Kiebel et al., 1999, NeuroImage (, but even if I take the residuals (ResMS.img), I get different values. SPM unfortunately doesn’t show the values for individual masks, but only for the whole brain.

Moreover, I wonder what you would take as input for FWHM as input for alphasim. The mean of FWHMx, FWHMy, FWHMz?

Thanks a lot for your help in advance!


PhD Student
University of Leipzig
Department for Psychosomatic Medicine