Dear FreeSurfer experts,

 

I am currently conducting a research project in which I am using 7T MP2RAGE data. I have denoised all the images and have used the -hires flag in FreeSurfer version  6.0.1 but for one images the skull stripping is not great and there is still some skull left. I tried using different preflooding heights, as stated on the website, but this resulted in parts of the brain being cut off.  I then tried to manually edit the brainmask.mgz  using tkmedit but in every other slice the skull still remains (as seen in the attached image). Is there a way to fix this in tkmedit or do you have any other recommendations?

 

I also wanted to ask if there is a way to bypass the bias correction step in the expert options file? And can the solutions to the two aforementioned issues also be applied to newer version of Free Surfer, specifically FreeSurfer version 7.4.x?

 

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

 

Thank you in advance.

 

Kind regards,

Kirsten