On 8/8/18 2:17 PM, Funk, Quentin wrote:
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Freesurfer experts,
I'm trying to figure out what values I get from mri_glmfit as in the
tutorial.
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>In
particular, I'm interested in how I can compare these values to what I
get from QDEC.
QDEC runs mri_glmfit, so they will be the same assuming you give it the
same input, design, and contrast.
In that tutorial, the software does a linear regression for each
gender and then computes a F_ratio for the two two fits. (How does
this relate to the average in the contrast listed?)
If the average were 0, then you would have no result whereas the F test
will test for any combination of the two
The F_ratio then gives a way to get P-values (under certain
assumptions)--so then from the F_ratio, pvals are computed--this leads
to sig.mgh.
But what are the other files? The descriptions are a bit too vague for
me to understand, unfortunately. The ones I'm interested in primarily are:
pcc.mgh -- partial (pearson) correlation coefficient (surface overlay)
Do you know what a pearson correlation is? The pearson can only be
computed between two sets of numbers. When you have multiple regression,
you use a partial pearson.
z.mgh -- z-stat that corresponds to the significance (surface overlay)
This is the p-value converted into a z.
The z-stat should be some sort of standard score--so a standard score
of significance (so p-value?) compared to what distribution?
Second, what if I were interested in a different categorical
variable--say I had a group of Alzheimer's patients and a group of
Healthy patients. In QDEC, I click "diagnosis" as the variable to do
the analysis on. What contrast does this correspond to? What type of
linear fit is being compared--the slope of the regression with respect
to age? If I leave out nuisance variables (like age), I should
conceivably get an F-test between the two constant models, which
should be more or less similar to a voxelwise t-test?
The contrast will be [-1 +1]. The sig.mgh will be the sig of the t-test
(ie, a signed test).
Any help here is appreciated!
Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003 <tel:713-363-9003>
Houston Methodist. Leading Medicine.
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