Dear freesurfer community,
we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have been experiencing a problem with the automatic recognition of the control points. After setting the control points and running autorecon2-cp white matter segmentation is faulty in almost every slice. I attached screenshot of two slices.
Can you recommend us a procedure to improve the automatic recognition of control points?
Below, we provide the details of our setup.
Feel free to ask for more information. Thank you very much for your help!
Yours sincerely,
Annemarie
$ bugr
FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Debian version: 5.0.6
Kernel info: Linux 2.6.27.39-1-ql-beowulf i686
$ which freesurfer -> /apps/prod/i486/freesurfer -5.3.0/bin/freesurfer
Used command:
recon-all –autorecon2-cp –subjid ET39_mdeft.
