Should have mentioned, that using the ResMS approach works in AFNI. In SPM,
you need to use [n 1] for the 3rd argument to get an approximation - where
n is the number of images in the original model. This corrects for not
passing all of the residuals.
On Mon, May 18, 2015 at 4:28 PM, MCLAREN, Donald <[log in to unmask]>
wrote:
> Alternatively, the square root of the ResMS.img image gives you a good
> approximation of the smoothness as well.
>
> In the line:
> s_mm=FWHM_est*1.5
>
> 1.5 is the voxel size, so if you are using a different voxel size, you
> should replace this number with the correct number(s).
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital
> and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
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> On Mon, May 18, 2015 at 6:32 AM, Katharina Wittfeld <
> [log in to unmask]> wrote:
>
>> 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
>>
>
>
