Hi Doug and Bruce

Well, now I am confused!

Please find attached an example of what the data looks like for FWHM of 1, 3, and 6mm kernel. The 1 (i.e. barely smoothed) looks pretty bad in my opinion. The FWHM of 3 captures the two peaks I see in my volumetric maps. The FWHM 6mm smooths this to one peak. I was therefore worried that 6mm is too much a smooth.

The idea is to illustrate something like the following maps

http://onlinelibrary.wiley.com/doi/10.1111/j.1460-9568.2012.08109.x/full

Unfortunately no information on smoothing is given in this article.

Best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, May 24, 2017 at 5:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
I guess I can't really advise you since I don't understand the
application. what will you do with this smoothed map? There is no fixed
smoothing kernel applicable for volume or surface-based analysis.
Usually it depends on the spatial extent of the effect you are looking for.


On 05/24/2017 05:39 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I'm doing just that - creating a statistical probability map to look
> at the overlap across the 40 subjects for a given sulcus. When we do
> this volumetrically it is traditional to smooth using FWHM of 3mm
> (about the width of a sulcus). *I was told for surface data it needs
> to be more than this, but I do not want to over-smooth.*
> The command you gave me to do this back at the workshop in September
> was mris_fwhm. I just wanted to know what an acceptable FWHM value
> would be.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, May 24, 2017 at 5:08 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     not sure what you are trying to do or why you would want to smooth the
>     prob map
>
>
>     On 05/24/2017 05:03 PM, Trisanna Sprung-Much wrote:
>     > Hi there
>     >
>     > I labelled sulci in 40 T1 volumes and have created surface overlays
>     > using mri_vol2surf and then registered these to fsaverage using
>     > mri_surf2surf. I want to generate a statistical probability map
>     using
>     > mri_concat and then mris_fwhm for each sulcus. What is an acceptable
>     > FWHM to use? It is the width of a sulcus on a pial surface of an
>     > individual brain, i.e. about 2mm? Or on fsaverage, i.e. about 7mm?
>     >
>     > Thanks
>     > Trisanna
>     >
>     >
>     > --
>     > Ph.D. Candidate
>     > McGill University
>     > Integrated Program in Neuroscience
>     > Psychology
>     >
>     >
>     >
>     >
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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