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 <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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