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 > 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.
