Dear Freesurferers

I was trying to do a connectivity analysis using subnuclei of Amygdala.

I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked at the results, the values are too high (around 800). Could you please let me know what I'm doing wrong?

P.S: the segmentation was basically done in MNI152-1mm and I moved it to MNI305-2mm by mri_vol2vol.

mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade

mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt

Thanks a lot

MOna