Dear Freesurfer Developers,
I am trying to segment the grey matter and pial surface using the FreeSurfer command recon-all with the hires flag. But even though there is no error while executing my code, when I analyze the output surfaces, the segmentation is missing some areas in the brain (I attached an image to show these brain regions).
My command is:
recon-all -all -s $SUBJ -hires -i $IMAGE -expert $EXPERT_FILE
My expert file contains:
mri_em_register -p .5 mris_fix_topology -s 50 mris_inflate -n 100
Does anyone have any thoughts on how to troubleshoot my problem?
Thanks in advance,
Gio.
1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. u-name -a: Linux ubuntu 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
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