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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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
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hmmm, I agree with Doug. Why would you want to smooth? The probability maps will have their own smoothness, which will reflect how well they register across subjects
cheers Bruce On Wed, 24 May 2017, 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 [cleardot.gif]
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Wed, May 24, 2017 at 5:08 PM, Douglas N Greve 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 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/
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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.
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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>
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-- 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/
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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
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Trisanna Sprung-Much