Thanks so much Doug, this makes sense to me now. Just to confirm, this value (contained in the fwhm.dat file) represents the actual filter width the analysis used in qdec, not what I initially specified (which was a 10 mm fwhm) in my design, is that correct?

I also have one more related question. In order to run 3dClustSim in AFNI I need to create a mask of each hemisphere for my study specific averaged brain (which I used in my qdec analysis) along with the effective fwhm filter width (13.990453).  Initially, I was thinking to use the lh.surface and rh.surface files (mri_label2vol) and convert them to .mgz format and then to .nii (mri_convert). At that point I could then create an averaged mask for each hemisphere, but now not so sure if that even makes sense.

Could you advise me on the most efficient way to accomplish this?


Thanks!

On Tue, Dec 8, 2015 at 5:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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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Douglas N. Greve, Ph.D.
MGH-NMR Center
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