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 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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer