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
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 thefunctional 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
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 thefunctional 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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Hi Adam, there is an example of this on the FreeSurfer wiki. Search for FSGD and look for the One Group, One Covariate in the FSGD Example page.
doug
Adam Nitenson wrote:
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 thefunctional 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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
freesurfer@nmr.mgh.harvard.edu
-
Adam Nitenson -
Douglas N Greve