Re: [Freesurfer] Creating Brainmaps for Significant Regression

Hi Doug,

Ok this makes sense, I just am unsure as to how I should create my contrast (.mtx) file. If I have 1 class and 3 levels of 1 continuous variable (3 allele loads: 0,1,2) how would I structure the contrast file to answer the question, "Is there a significant linear relationship between allele load and functional activation/deactivation?

My fsgd file will probably look something like this:

GroupDescriptorFile 1 Title Alleles Class Patient Variables AlleleLoad Input Patient1 Patient 1 Input Patient2 Patient 2 Input Patient3 Patient 3

(etc)

Thanks,

Adam

This is a standard type of group analysis using a single covariate. You can set up an FSGD file specifying the groups as classes and using allele load as a continuous variable. If you're not interested in the differences between the slopes, then use a DOSS model when you run mri_glmfit. Search for FSGD on the wiki for more info.

doug

Adam Nitenson wrote:

...

Hi all,

So far I have only been using Freesurfer analyses to look at the

functional activation for individuals, single groups, and subtractions between 2 groups. We now want to investigate a possible linear relationship between allele load (Three levels: 0,1,2) and functional activation. Is there a way to create a brainmap using glmfit or some other command that displays voxels that display a significant regression of genotype (such as red for positive / blue for negative linear relationship)? Basically, it would be a map that shows significant "r" instead of significant difference.

Thanks,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital