You could extend the analysis described on that wiki page by calculating tstats
and pvalues (in addition to mean and stdev). Then you have a paired t-test,
whereas mri_glmfit with qdec would be doing an unpaired t-test. I think
preproc has an option to calculate within subject differences for a paired
t-test with mri_glmfit as well. As you may know, paired t-tests are more
sensitive than unpaired t-tests, and are generally more appropriate when you
make within subject comparisons. On the other hand, if you intend your
exercise to be a test for the likelihood of false positive differences between
groups, the unpaired t-test may be more appropriate.
> Subject: Re: [Freesurfer] qdec thickness and repeatability
> From: ni...@nmr.mgh.harvard.edu
> To: bell0...@umn.edu
> Date: Fri, 20 Feb 2009 15:15:10 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
>
> The two methods are very different. In the method described on the
> thickness repeatability page, its computing a mean and stddev of the
> thickness for your group. This a direct and easily interpretable
> measure, but doesn't give you a statistical measure (but you could do
> that on your own with some external package).
>
> In qdec (mri_glmfit), it would be conducting a GLM-based analysis
> looking for statistical significance, expressed as a p-value at each
> vertex, in thickness between groups. Here, raw thickness differences
> are hidden in the analysis.
>
> However, you can of course do both analysis, and compare them, which I
> would suggest you do. You would hope the areas of change are the same.
> Note that you can load external surface maps, such as a thickness-
> diff.mgh map, onto the fsaverage surface in qdec, so that you can view
> both analysis (or just load the thickness-diff.mgh map in tksurfer).
>
> Its on the list of things to add to qdec to create two-group thickness
> difference maps, as well as just viewing the mean group thickness, to
> save some work for this sort of thing.
>
> Nick
>
>
> On Fri, 2009-02-20 at 12:53 -0600, bell0...@umn.edu wrote:
> > All,
> >
> > I am going to run an analysis of cortical thickness reproducibility; there
> > are at least two methods that seem obvious. I could run qdec analysis with
> > time1 and time2 as different groups or I could run the methods below. Are
> > the commands below the same ones used in the qdec GUI? As far as I can
> > tell, they will both give me cortical thickness differences on a vertex by
> > vertex basis. There are probably some subtle differences in the way they
> > are coded, but any major changes? Thanks.
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
> >
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> >
> >
>
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