Reschke, Cole wrote:

Thank you, I have three follow up questions:

Threshold is –log10(p), why are negative values showing up on the display?

Sorry, the formula is not quite right, it is -sign(t)*log10(p), where t is the t ratio for the t-test. It's sign is the sign of the contrast.

I am using fsaverage to display my results, would it make any difference if I created my own average subject based on the analysis?

It won't really have an effect on the analysis.

Is it possible to export the voxel-by-voxel intensities (or the brain surface data) used in Freesurfer’s analysis; and then re-import the some external analysis results back to Freesurfer format for display purposes?

Yes. The input to mri_glmfit (ie, arg of --y) is just such a file. If you make your analysis have the same size and don't swap the voxels around, then you can can reimport.

dopug

Cole

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve
Sent: Monday, January 22, 2007 11:56 AM
To: Reschke, Cole
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] interpret analysis results

The values are -log10(p), so p < .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial.

doug

Reschke, Cole wrote:

First, thanks to Doug for all his help up to this point.

Next, I have three questions. In my analysis, I used the –paired-diff and –osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface.

Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)?

I adjust the threshold by changing the ‘Min’ value in the ‘Configure Overlay Display’?

Ex. If Min ==3, then p < 0.001 ?

Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)?

Thank you,

Cole

Cole Reschke

Data Manager, PET Center

Banner Alzheimer Institute

Banner Good Samaritan Medical Center

Phone: (602) 239-4868
 
 
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting