3dcalc -a ResMS.hdr -expr 'sqrt(a)' -prefix sqrt_ResMS.nii
-->produces a residual image of the data
3dFWHMx -mask yourmaskfile sqrt_ResMS.nii -->produces the
smoothness of the data in mm, output is used below for -fwhmx # etc.
AlphaSim -mask yourmaskfile -fwhmx # -fwhmy # -fwhmz # -pthr .005 -rmm
.71 -iter 2000 > tmp.txt -->produces a text file that determines the
cluster size
.005 is the voxel significance value and can be changed.
.71 is the connectivity radius, we typically use edge-connected
voxels, so its slightly larger than sqrt(voxel_width ^2+voxel_length
^2) assuming isotropic voxels, the above was for a monkey study with
.5mm isotropic voxels.
Hope this helps.
Best Regards, Donald McLaren
=================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Office: (608) 520-0586
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On Mon, Aug 2, 2010 at 3:06 PM, Patrick Pruitt <[log in to unmask]> wrote:
> 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
>
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