Try, smoothest -r stats/res4d.nii.gz -m BrainMask_05_61x73x61.hdr -V
This should give you 3 values in voxels, which can be converted to mm
for use with AlphaSim. The numbers should be pretty close between the
two programs.
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, Aug 13, 2012 at 11:11 PM, Jessica Andrews-Hanna
<[log in to unmask]> wrote:
> Hello!
> I’d really appreciate if someone might be able to offer some insight into the following questions.
>
> I would like to use AFNI’s AlphaSim/3dClustSim on fMRI data processed with FSL. It is my understanding that the smoothness required as input to AlphaSim should refer to that estimated from the residual fMRI data (i.e. the “res4d.nii.gz” image). In order to estimate smoothness of my dataset, it seems I have two choices. I could use the FSL program, “smoothest,” or the AFNI program, “3dFWHMx.”
>
> However, I am a bit confused as to why I get very different smoothness calculations from these two programs. 3dFWHMx consistently yields much larger FWHM kernel sizes than smoothest.
>
> For example, when I run
>> 3dFWHMx –input stats/res4d.nii.gz –mask mask.nii.gz
> I get FWHMx values of x=10.342, y=10.6017, z=9.72374
>
> On the other hand, when I run
>> smoothest –r stats/res4d.nii.gz –d <degrees of freedom> -m mask.nii.gz
> I get RESELS = 319.143, which corresponds to FWHM of 6.8337 (cubed root of 319)
>
> Furthermore, when running "smoothest" on residual data, a flag for degrees of freedom is required. However, the different dof inputs produce the exact same “resels” value. If this value isn’t being used, could it reflect a possible bug?
>
> Any insight would be much appreciated. Thanks!
> Jessica
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