Naveed Wrote:
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> Is this function works similar to this command>>
>
> [naveed-centos@localhost CNT02.results]$
> 3dBlurToFWHM -FWHM 10 -automask -prefix
> conn_smooth -input Connectivity_mask_anat+tlrc

Almost always the input data already has some smoothness, in which case they are not identical:
- 3dBlurToFWHM smooths the data *until* it has reached a certain smoothness
- 3dmerge will smooth the data with the given smoothness

Also, for 3dBlurToFWHM it is important that the -blurmaster dataset (or the input dataset, if -blurmaster is not given) has no anatomical structure. I don't have much experience with connectivity-based analyses, so this may or may not be the case for your data. How did you preprocess it?

> I couldn't find any significant change by running
> this one.

You can estimate the resulting smoothness from both approaches using 3dFWHMx.