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.
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
[IMAGE]
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
