Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab? Would this be problematic with a different smoothing procedure in mri_glmfit? How will mri_glmfit deal with the longitudinal design? Does this matter, or the FWHM would only be estimated on a average image of all time-points for all subjects? Regards, Pedro Rosa.
On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: > > I think I would just run mri_glmfit on your data to get the proper directly > structure and estimate of FWHM, then copy the sig file from the mixed fx > analysis into the glmfit folder for one of the contrasts. Then run > mri_glmfit-sim. > > doug > > > On 3/29/14 10:29 AM, Pedro Rosa wrote: > > Dear Doug and Jorge, > > Thank you very much for your help. > > I found another message in the list > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) > > in which you suggested a way of using MC in mri_glmfit-sim by creating > > “fake files”, which would not be read by the script. In this case, only the > > simulation would be run, and not the full statistics. The command would be > > something like this: > > - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign > > abs > > I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested > > by the older post. This would be fine, I believe, if only sig.mgh is read > > by the script. > > However, I get this message after running the command: > > [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim > > --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs > > if: Expression Syntax. > > > > Is it possible to do what I am trying to do? Does the residual errors at > > each location included in the sig.mgh, and, if necessary, how to compute it > > into image FWHM? > > Regards, > > > > Pedro Rosa. > > > > > > On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: > > > > > 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 (mailto: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) > > > > <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) > > > > <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) > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > 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 > > > (http://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 (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > _______________________________________________ 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 (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. > >
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