Re: [Freesurfer] Generating a fsgd file for regression analyses

It is not a question of number of conditions, it is a matter of how you expect the outcome variable to change with input. By coding some scanners as 1 and some as 3 it means that you expect the outcome variable to change by a factor of 3 between the two scanners, probably this makes no sense. doug

On 07/15/2013 02:04 PM, Avram Holmes wrote:

Doug,

Thanks for the quick response. Scanner refers to site (e.g., Harvard, McLean, MGH Bay4, MGH Bay6, etc.) console refers to the console software version (e.g., B13, B15, B17. etc.). Any advice on how many conditions a class can have before I should code it numerically?

Avram

On Mon, Jul 15, 2013 at 1:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Avram, it basically looks ok, but I'm confused about the "scanner"
regressor. If these are two different MRI scanners, one at 1T and
one at
3T, you should probably make different classes for them. Perhaps the
same thing for the Console variable.

doug


On 07/15/2013 01:19 PM, Avram Holmes wrote:
> Freesurfer et al.,
>
> I'd like to try out some simple cortical thickness regression
analysis
> in mri_glmfit. These would be analyses of one continuous score
(e.g.,
> Temperament) and several continuous nuisance variables (e.g.,
Age, IQ,
> Site, etc). However, before getting started I wanted to run my fsgd
> and contrast files by the mailing list to make sure I am entering
> things correctly. If any freesurfer pros have a free moment I've
love
> to hear if I am on the right track.
>
> My fsgd file looks like the following:
>
> GroupDescriptorFile 1
> Title
> Temp
> MeasurementName thickness
> Class Main
> Variables  Temperament Age Scanner Console IQ
> Input
> Subj1
>  Main -2.65 22 3.00 4.00 103.0
> Input Subj
> 2
>  Main -2.24 24 3.00 3.00 109.0
> Input Subj
> 3
>  Main -1.82 20 1.00 4.00 121.0
> Input Subj
> 4
>  Main -1.79 19 3.00 3.00 113.5
> Input Subj
> 5
>  Main -1.77 19 1.00 3.00 101.
> 6
> ....
>
> My contrast1.mat file is:
>
> 0 1 0 0 0 0
>
> It is my hope that when I call:
>
> mri_glmfit --fsgd GLMFIT/fsgd.txt --y GLMFIT/lh.TEMP.mgh --C
> GLMFIT/c.txt --surf fsaverage lh --cortex --glmdir
GLMFIT/lh.TEMP.output
>
> I am prepping to run a regression looking at the relationship
between
> Temperament and cortical thickness, partialing out age, scanner,
> console, and IQ.
>
> Thanks in advance for any help you can offer,
> Avram
>
> --
> Avram Holmes PhD
> Instructor in Psychiatry, Harvard Medical School
> Assistant in Research, Massachusetts General Hospital
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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-- Avram Holmes PhD Instructor in Psychiatry, Harvard Medical School Assistant in Research, Massachusetts General Hospital