*By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote: > Dear Doug, > > Finally I've got it. But there is one more problem: when I run the > QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I > am running the results from QDEC(under Untitled.glmdir) with the -sim: > > mri_glmfit-sim \ > --glmdir Untitled.glmdir \ > --cache 2 pos \ > --overwrite > > I am getting only one of the clusters. Can you please advise me what > is going on or what should I correct? > > Many thanks, > AK > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com>; freesurfer > <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 1:33 PM > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > again, FDR should have nothing to do with it. If you want a voxel-wise > threshold at 2, just set that threshold when you run mri_glmfit-sim > with "--cache 2 sign" where sign is pos, neg, or abs > doug > > Antonella Kis wrote: > > Hi Doug, > > > > Thanks again for helping. I am trying to use QDEC but there are no > clusters surviving after FDR (it says statics cannot be done so gives > me error by running FDR). So I am trying to get the thickness values > only for the clusters that are formed in QDEC after setting up a > threshold = 2 (before running FDR). In order to do this you suggested > me to run mri_glmfit-sim on the QDEC results. The only problem is that > I cannot run the -sim if there is no FDR data (stats) so I cannot > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > do it? > > > > Many thanks, > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com>> > > *Cc:* "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, September 28, 2011 12:06 PM > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > What does FDR have to do with it? FDR should not come into play in this. > > doug > > > > Antonella Kis wrote: > > > Good morning Doug, > > > > > > I tried running the -sim on my QDEC output (as you recommended me last > > > days) but for some data the FDR gives me error (cannot calculate > > > clusters statistics) so mri_glmfit-sim is not working either since the > > > corrections by multiple comparisons is not working. What should I do > > > in this case so I can get as output my cortical thickness values for > > > the formed clusters at threshold 2, before multiple comparison? > > > > > > Many thanks, > > > AK > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > >
-- 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
