Re: [Freesurfer] 3dClustSim and Gaussian filter width

Yes, we assume isotropic, but it is on the surface so xyz do not apply

On 12/08/2015 05:43 PM, Emma Thompson wrote:

Thanks Doug. I located the fwhm.dat file in my qdec output folder for the analysis I'm interested in. I see only one number (13.990453) in this .dat file, I was expecting three numbers corresponding to x, y, z directions. Do I assume this is isotropic then, that is: 13.990453 x 13.990453 x 13.990453?

On Mon, Nov 30, 2015 at 11:23 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

look in the glmfit output folder for  a file called fwhm.dat



On 11/29/15 3:06 PM, Emma Thompson wrote:

...

Sorry for the repost of my last post, but I now realize that what
I need is the estimated filter width that was actually used in
the qdec analysis not the fwhm that I actually specified, i.e. 10 mm


http://afni.nimh.nih.gov/afni/community/board/read.php?1,66182,66190#msg-66190


On Sun, Nov 29, 2015 at 2:51 PM, Emma Thompson
<voneconomos@gmail.com <mailto:voneconomos@gmail.com>> wrote:

    Dear Freesurfers,
    I am reposting my message in hopes that someone will reply
    this time around - still grappling with this problem. Thanks.



    On Tue, Oct 27, 2015 at 8:59 AM, Emma Thompson
    <voneconomos@gmail.com <mailto:voneconomos@gmail.com>> wrote:

        Dear Freesurfers,
        I am trying to use 3dclustsim in AFNI to determine the
        minimum number of voxel in a cluster to reach
        significance, my understanding is that in the command
        line the -fwhm s flag refers to the gaussian filter width
        and NOT the Gaussian Kernel, can anyone point me to how I
        might be able to obtain this for each hemisphere in
        freesurfer? I am using my own average brain that I
        created, but it would help to know how to do this for the
        fsaverage as well.

        Many thanks for your help!


        http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html





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