yes, though I would probably do it outside of qdec as it can take a while (hours or days)
On 06/12/2012 08:03 AM, Marie Schneider wrote: > Thank you very much for your answer. > > Are 10 000 iterations also used when I am running a Monte Carlo > simulation in qdec? > > Thanks, Marie > > 2012/6/9 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > they are two different correction schemes. If they gave the same > answer, > then it would not make sense to have both. the monte carlo tries to > compute the probability of a cluster of the given size under the null > hypothesis. FDR controls for the number of false positives relative to > the total number of positives under the assumption that if any 5% of > your positives are false, then you would not change your conclusion. > > For monte carlo, we generally use 10000 iterations. If you are > using the > whole hemisphere, then you can used the cached tables. See the > "command-line" tutorial. > > doug > > On 06/08/2012 08:03 AM, Marie Schneider wrote: > > Dear FreeSurfer experts, > > > > I have some questions about corrections for multiple comparisons in > > FreeSurfer. I have two samples, one consisting of two groups and one > > consisting of three groups. > > > > I do the comparison with the sample of two groups in qdec. > Correcting > > for multiple comparisons, I get a significant result using FDR, > but no > > significant result using Monte Carlo simulation. How can that be? > > > > I analyze the sample with the three groups by mri_glmfit. In your > > tutorial, I only found how to correct for multiple comparisons with > > the Monte Carlo simulation using the command line, but not how to > > correct with FDR using the command line. Is there a possibility > to do > > this? If not, how many iterations are usual to use within the Monte > > Carlo simulation? > > > > Any help is appreciated. > > > > Thank you very much, > > > > Marie > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > -- 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
