Hi Gio,
did you check the output of the skull stripping? It is the most likely culprit. It's hard to tell from those images, but if the lateral cortex gets significantly darker than more medial stuff (which happens at high field) you might need to add some control points in the white matter of the region that was excluded. It would also help if you gave us some details of the acquisition. What field strength? Was it prescan normalized? Is there a body coil?
cheers Bruce
On Thu, 11 Jan 2018, Giovana dos Santos Cover wrote:
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.
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
- 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
[IMAGE]