[Freesurfer] Issue with cortical data extraction for mkanalysis-sess

We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but for the right hemisphere, something is clearly off. When we export the results into a table, the unknown column, which should be zero, has values, and one of the regions instead has zeroes. It’s as if something is shifted, but we’ve checking the coding. Briefly, the commands we used were mri_vol2vol, fcseed-config, fcseed-sess, mkanalysis-sess, selxavg3-sess, mri_glmfit, mri_segstats. Any ideas on where/which commend we should be troubleshooting? We’ve run it twice and gotten the same results.

Thanks, Sarah