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