You're almost there, Beth. When you run mri_surfcluster, specify the --ocn output. This will create a 'segmentation' with each value being the number of the cluster. Then use mri_segstats specifying the ocn as the segmentation and the cluster number you want as the segid. Also specify and output 'waveform' file with --avgwf. This will output a text file with the values you want. doug

On 3/10/11 8:43 PM, Beth Mormino wrote:

Hi Surfers!

I have done a group level analysis relating a variable to thickness values. I have a sig.mgh file that shows the relationship between the variable and thickness at each vertex. Now I would like to threshold the sig.mgh file (at values of 3 and above), and then extract an average thickness value across this entire mask for all my subjects. I have been able to convert the sig.mgh to an annotation using mri_surfcluster, but this file contains multiple clusters when all I'd like is 1 mask. Once I get to this step, I assume there is a way to then extract thickness values using the thickness.mgh file originally fed into mri_glmfit, but can't seem to get this to work with mri_segstats. My solution has been moving the annotation back into each subject's space with mri_surf2surf, but this seems like a very round-about way of completing this analysis.

Thanks in advance! Beth _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer