Hi Evert,
one thing you can try if the patterns of loss are stereotyped is to take 10 or 20 subjects or so and correct them by adding control points, then use mri_compute_bias to compute the common component of the bias field. You can then apply that to the other subjects in your study with mri_apply_bias. Nick can probably suggest a good way to slot this into the recon-all process.
cheers Bruce
On Thu, 29 Oct 2009, Evert van Velsen wrote:
Hi Freesurfer users,
As nobody responded the previous time, I send my question again. I am trying to reconstruct the surfaces of 1.5T images that I have (n>800). In almost half of my images, minor portions of the temporal lobe (and in some also the orbitofrontal lobe) are missing (e.g. see images attached). Has somebody any suggestions how to solve this problem in an easy way (FreeSurfer settings e.g.), as it is (almost) impossible to add control points for all subjects. If you need some data to get more information about our problem, please let me know.
Thanks in advance,
Evert