Hi,
I ran autorecon1 on a group of data consisting of a single set of mprage DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of the brainmask.mgz images had large portions of the brainstem and cerebellum removed. A couple had portions of the neck which were not removed. The talairach transforms looked fine.
A more experiened Freesurfer user suggested that adding control points and re-running the intensity normalization might fix this. I assume that I can follow the instructions here,
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fControlPoints
but that I would need to edit the orig.mgz file and then run autorecon1-cp. Is this correct?
My intended analysis (cortical thickness in PFC regions) does not depend upon these flawed regions, but I want to make sure these errors aren't indicative of some larger problem. Also, I know there have been issues with gradient warping with the Allegra. Do these problems sound like gradient warping symptoms?
Thanks, Cate