---

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, August 23, 2011 4:33 PM
Subject: Re: [Freesurfer] correction for multiple comparisons

Yes, that is correct, you should use .025 if you are correcting for both
hemispheres.
doug

Antonella Kis wrote:
>
> Hi Doug,
>
> I would like to run the correction for multiple comparisons. I know
> glmfit-sim corrects for multiple comparisons. My question is:
>
> the corrections for multiple comparisons will be done while running
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --overwrite
>
> or I need to add --cwpvalthresh .025 before --overwrite. I found
> on-line that  setting a treshold = 2 means  p < 0.05 but adding
> --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh:
> .025 = .05/2
> Bonferroni Correction and will show only the clusters with p<.025.
> 
> Is this right? So to run for multiple corrections in fact I will need
> to run:
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --cwpvalthresh .025
> --overwrite
>
> Please advise me.
>
> Thank you for your time and help.
> Antonella
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <atorok9@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Monday, August 22, 2011 2:28 PM
> *Subject:* Re: [Freesurfer] GLM or Qdec ?
>
>
>
> Antonella Kis wrote:
> > Dear FS experts,
> >
> > I finished running the GLM and I wonder what is the best way to
> > further analyse my data in order to see if there is any relation
> > between age (at seizure onset) and cortical thickness for my  patients
> > versus control group.
> >
> >
> > 1).  Why when I overlay the sig.mgh in tksurfer lh inflated, I get
> > more clusters than the number of clusters obtained from mri_glmfit-sim?
> When you look at it in tksurfer, you are looking at uncorrected data.
> glmfit-sim corrects for multiple comparisons. Some of the clusters don't
> survive.
> >
> > 2). What sig.mgh represents?
> -log10(p)
> >
> > 3) What's the real significance of a  cluster (how a cluster is formed)?
> It is based on the likelihood of getting a cluster of that size by
> chance given the search space (cortical surface area), smoothness
> (FWHM), and cluster-forming threshold (eg, p<.05).
> >
> > 4). Why my thickness value in clusters (eg cluster no. 1 which
> > coresponds to the posteriorcingulate) for subject no.1 is different
> > that the thickness value obtained for the same region in the
> > lh.aparc.stats while running recon-all?
> >
> > 5). After running the GLM should I use visualizing and plotting method
> > to further analyse my data  and load FSGD file
> > lh.gender_age.glmdir/y.fsgd?
> >
> > 6). Should  my ROI's be defined or be the same with my clusters?
> I don't know what you mean by that.
> >
> > 7). What is the difference between GLM and Qdec? What method is the
> > best to analyse the relation between age  and cortical thickness for
> > my  patients versus control group?
> They are the same statistically. They are just different ways to provide
> information about your design and contrasts. QDEC is graphical (point
> and click). mri_glmfit you create FSGD files and run it from the
> command-line. QDEC actually creates FSGD files and contrast files and
> runs mri_glmfit.
> >
> > 8). Why when analysing with Qdec I get more clusters? Are this
> > defining or representing the sig.mgh as in GLM?
> They should give identical results when run in the same way. My guess is
> that you have created two different designs and so are getting different
> answers.
> >
> > 9). When using Qdec were I can find as an output of results  the
> > number of clusters and the cortical thickness value?
> You'll have to run the correction for multiple comparisons (interface on
> the results page). This simply runs mri_glmfit-sim.
>
> doug
> >
> >
> > Thank you and have a great day!
> > Antonella
> >
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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

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