Hi Freesurfer team, I am trying to get intra-rater reliability statistics on an ROI manually traced twice (blindly). The scans are anisotropic (.38 x .38 x .8 mm) and so I have not run them automatically through the Freesurfer segmentation because they fail after autorecon1. I tried to use the following command but have had problems: mris_anatomical_stats -a ${s}/label/${h}.aparc.annot -f cortical_thickness_stats/${h}_${s}.txt $s $h
It seems this command requires certain data from the autorecon process such as wm.mgz and other surface information that I cannot get because autorecon fails on these types of scans.
I have only traced one hemisphere (the Left) and the ROIs are saved as label files; an example is: /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV126/ whole_amygdala.label
Is there another way to get reliability (pixel overlap, total number of pixels, etc.) for two ROIs? Would you suggest another command or is there a way to bypass those requirements for the mri_anatomical_stats command?
Thanks!