Hi Lucia, you can do this from the terminal window. cd into the glm output directory and you'll see a beta.mgh file that has all the beta values. You can use

mri_segstats* --i beta.mgh --slabel fsaverage lh youlabel.label --id 1 --avgwf avgwf.dat or *mri_segstats* --i beta.mgh --annot fsaverage lh aparc --avgwf avgwf.dat

The avgwf.dat file will have a separate column for each parcellation (only one for the slabel). There will be a row for each beta.

doug

* Lúcia Garrido wrote:

Hello,

I'm trying to extract beta values in cortical thickness analysis. For example, if I use qdec to look at the association between cortical thickness and variables A and B, can I extract the vertex-wise parameter estimates corresponding to the association between A and cortical thickness across subjects for a certain ROI? This ROI could be one of the regions from freesurfer parcellation or another saved ROI.

I can visualize the beta values by looking at beta.mgh in tksurfer but I'd like to be able to extract them in 'table' format. I think I know how to do extract summary statistics for an ROI, but I'd like instead to extract the betas for each vertex.

Many thanks for your help!

Lucia

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