Hi Trisanna
let's take a step back - what exactly are you trying to achieve? If it is
to make a map of the probability that a fold occurs at a specific location
then you should not be smoothing at all. And I don't understand why you
would be labeling a fold in the volume - why not just label it on the
surface (since it is a property of the surface)?
cheers
Bruce
On Wed, 24 May 2017,
Trisanna Sprung-Much wrote:
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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, May 24, 2017 at 5:43 PM, Douglas N Greve <gr...@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
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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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