Dear Lilla,

Thank you very much for your answer and your help. I followed all the recommended steps (I introduced a white matter mask that will ensure that I am  only
considering diffusion values in the white matter and then also I did corrected for multiple comparison running mri_glmfit-sim with the option grf as Doug recommend me).

My question is how can I conclude if there is an increase and/or decrease in the FA values in one group (for example Patients) versus another group (example controls).

In other words can we conclude on the FA values based on the GLM results/clusters  from the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion (I don't see anymore the image with red and blue clusters posted on this website. Is something going on?)


Thank you very much!
Antonella

From: Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, December 13, 2011 12:02 PM
Subject: Re: [Freesurfer] FA interpretation from cvs registration for group analysis

Hi Antonella,

> I will appreciate a lot if you can help me understand what is the meaning of the results after running after running mri_cvs_register and the GLM group analysis.
>
> More exactly, I followed all the instructions from the webpage:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion
>
> and I wonder if based on the cluster's colours I can say something about my FA values in one group related to the other one.
>
> More exactly I am looking to understand if I have an increase in the FA value for the controls versus patients or the FA in patients is larger than in the control group.
>
> My contrast matrix is C = [+1.00000 -1.00000 ] and I have 30 controls and 32 patients.

I am not sure how to comment on your outcomes as I don't know anything
about your data. However, the diffusion tutorial that we put together is
a very top-level roadmap on how one might go about voxel-based analysis
of their diffusion data. It is not complete in a sense that you would
want to make sure that there is some further processing done on your data
sets before you start interpreting the results. One is that you would
want to introduce a white matter mask that will ensure that you are only
considering diffusion values in the white matter and then also you would
want to correct for multiple comparison running mri_glmfit-sim. We are
planning on updating this tutorial further for our next course to reflect
all these additional steps.

> What is the age range for the cvs_avg35 space? I wonder if is the best space to register my subjects if they are children with age between 6-14.

The atlas was constructed from 35 adults, consisting of males and females
ages 18 to 93.

We have been successul registering pediatric images also in that space,
but the outcome will also depend on the quality of your images.

--Lilla
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