Jorge, do you output the FWHM? doug On 03/27/2014 03:14 PM, jorge luis wrote: > Hi Pedro > > Sorry, right now the only multiple comparisons corrections implemented > in lme are the original Benjamini and Hochberg (1995) FDR procedure > (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure > (lme_mass_FDR2): > > Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear > step-up procedures that control the false discovery rate. Biometrika, > 93, 491-507. > > In my experience, this procedure is as powerful to detect effects in > neuroimage data as alternative corrections with strong control of the > family-wise error rate (FWE). However it would be great if we could > use an implementation of any multiple comparisons correction with > strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures > only provide weak control). The residual errors at each location > required to compute an estimate of the image FWHM can be obtained from > the lme output. But an actual FWHM estimate is not currently saved. > > Best > -Jorge > > > El Martes 25 de marzo de 2014 8:15, Pedro Rosa > <pedrogomesr...@gmail.com> escribió: > > Dear Doug, > Thank you very much! > I will try what you suggested, although I am not sure if Jorge's > stream outputs the FMHM, or if I would need to run the statistics > from the beggining using in the terminal, and not in MatLab. > Do you think Jorge could comment on this issue? > Regards, > Pedro Rosa. > > On Mar 24, 2014, at 12:44 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > In theory, it should be possible. I have not used Jorge's stream, > so I > don't know that much about it. Does it save an estimate of the > FWHM? If > so, then you can run mri_surfcluster passing it the p-value (ie, > -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. > This is > what mri_glmfit-sim does, so you might check that script for > mri_surfcluster command line options > > doug > > > > On 3/22/14 11:03 PM, Pedro Rosa wrote: > > Dear list, > > I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline > in a structural MRI dataset and I would like to use Monte Carlo as > the method for correction for multiple comparisons. However, the > longitudinal LME tutorial includes only FDR correction > (lme_mass_FDR2). > > Is it possible to use Monte Carlo correction for longitudinal > data? Can I input the outputs from MatLab (fstats = > lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and > then run Monte Carlo? > > If not, do you have any other suggestions of how I use Monte > Carlo in longitudinal analyses? > > Thanks in advance, > > _______________________________________________ > 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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: 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
