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Dear Andy,

I've only used Alphasim within the REST toolbox (which had a critical bug) and the current fixed version of it which was released within the DPABI Toolbox.

But the problem of smoothness estimation is the same in preparation to use one of these tools.

I found this website very helpful to keep the residual files for each person:
http://akiraoconnor.org/2010/03/24/keeping-residuals-after-spm-estimation/

To finally estimate the smoothness within a certain ROI I used the SPM function spm_est_smoothness:

% list with residual files
ResI_list = spm_select('List',dir_ResI,'^ResI.*\.img');

% and mask_path is the complete path to your mask defining the ROI

[FWHM_est] = spm_est_smoothness(ResI_list,mask_path)

% be careful which unit you need the smoothness to be in I needed it in mm and had to multiply it by the voxelsize.
s_mm=FWHM_est*1.5                  

If you don't need the residual files anymore, you can remove them:
    delete('ResI_*.img')
    delete('ResI_*.hdr')

I hope this helps you!

Best, Katharina