Hi,
Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters where my two groups differed (along with many other analyses, e.g. age slope for each group). For each cluster, I would like to see what the mean group difference is, in mm. So, I used this command:
mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --annot fsaverage rh ./mc-z.th1.3.pos.sig.ocn.annot
Unfortunately, mri_segstats looks in the wrong place for the annot file, prepending "$SUBJECTS_DIR/fsaverage/label/rh." instead of looking in my present GLM directory that I typed the command from.
In comparison, if I manually create a label for one of the clusters from the ocn.annot, and use the label, mri_segstats works:
mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --slabel fsaverage rh ./label.th1.3.neg/rh.cluster-001.label
This time, it doesn't try to look under fsaverage, but uses the present GLM directory. Is there a way to override the SUBJECTS_DIR issue with --annot? I tried without the "./", and with specifying the absolute path, but it still pre-pended the "$SUBJECTS_DIR/fsaverage/label/rh." before the path. Or, should I just create labels for each analysis, run mris_segstats for each cluster, and then combine them all back together with grep?
Thanks, -Kayle