[Freesurfer] Defining cluster threshold
Hi FreeSurfers, I have done my DTI analyses (dt_recon with TBSS) and the statistical analyses in FreeSurfer. Now I have defined the clustersize with mri_volcluster, but I find this rather arbitrary. Is there a way to calculate a minimum size cluster threshold (by using for example a Monte Carlo simulation)? Thanks! Heidi <><>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Defining cluster threshold
Hi Heidi, I'm not sure what you are asking for. Do you want to find a p-value for the cluster you have found in your TBSS analysis? If so, you can use mri_glmfit-sim to perform a simulation (monte carlo or permutation). doug Jacobs H (NP) wrote: > Hi FreeSurfers, > > I have done my DTI analyses (dt_recon with TBSS) and the statistical > analyses in FreeSurfer. > Now I have defined the clustersize with mri_volcluster, but I find > this rather arbitrary. > Is there a way to calculate a minimum size cluster threshold (by using > for example a Monte Carlo simulation)? > > Thanks! > Heidi > > > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Defining cluster threshold
Hi Doug, Thank for you answer. Let me clarify a bit more. I want to know if there is a statistical way to define relevant clusters (instead of doing a bonferonni correction). I can imagine that cluster with a few voxels cannot be considered as statistical significant. Heidi -Oorspronkelijk bericht- Van: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Verzonden: 06 October 2010 20:40 Aan: Jacobs H (NP) CC: 'freesurfer@nmr.mgh.harvard.edu' Onderwerp: Re: [Freesurfer] Defining cluster threshold Hi Heidi, I'm not sure what you are asking for. Do you want to find a p-value for the cluster you have found in your TBSS analysis? If so, you can use mri_glmfit-sim to perform a simulation (monte carlo or permutation). doug Jacobs H (NP) wrote: > Hi FreeSurfers, > > I have done my DTI analyses (dt_recon with TBSS) and the statistical > analyses in FreeSurfer. > Now I have defined the clustersize with mri_volcluster, but I find > this rather arbitrary. > Is there a way to calculate a minimum size cluster threshold (by using > for example a Monte Carlo simulation)? > > Thanks! > Heidi > > -- > -- > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 . 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
Re: [Freesurfer] Defining cluster threshold
Yes, for TBSS you probably want to use permutation simulation. BTW, why are you doing the group analysis in FreeSurfer? I think FSL offers TBSS group analysis. I'm not trying to steer you away from FreeSurfer, but it might make sense to stick with one software package. doug Jacobs H (NP) wrote: > Hi Doug, > > Thank for you answer. Let me clarify a bit more. > I want to know if there is a statistical way to define relevant clusters > (instead of doing a bonferonni correction). > I can imagine that cluster with a few voxels cannot be considered as > statistical significant. > > Heidi > > > -Oorspronkelijk bericht- > Van: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Verzonden: 06 October 2010 20:40 > Aan: Jacobs H (NP) > CC: 'freesurfer@nmr.mgh.harvard.edu' > Onderwerp: Re: [Freesurfer] Defining cluster threshold > > Hi Heidi, I'm not sure what you are asking for. Do you want to find a p-value > for the cluster you have found in your TBSS analysis? If so, you can use > mri_glmfit-sim to perform a simulation (monte carlo or permutation). > > doug > > Jacobs H (NP) wrote: > >> Hi FreeSurfers, >> >> I have done my DTI analyses (dt_recon with TBSS) and the statistical >> analyses in FreeSurfer. >> Now I have defined the clustersize with mri_volcluster, but I find >> this rather arbitrary. >> Is there a way to calculate a minimum size cluster threshold (by using >> for example a Monte Carlo simulation)? >> >> Thanks! >> Heidi >> >> -- >> -- >> >> ___ >> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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 . 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. > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
