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 smooththe
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 anacceptable
> 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
