Hi Ben
are the bright points segmented as wm in the wm.mgz? If so, you might try erasing them and rerunning
cheers Bruce On Wed, 31 Aug 2016, Benjamin Baird wrote:
Dear Freesurfer experts,
We are currently working with some scans that were collected on a GE 3T scanner. The goal is to analyze cortical thickness. The scans seem to be relatively high quality with the exception that there are what appear to be inhomogeneities in the intensity of the gray matter (appears too bright in places), which is causing the WM to extend/jump into cortex (see attached image). We're wondering if there are any parameter adjustments to recon that might help with this as the errors occur frequently enough that fixing them all manually will be fairly cumbersome. This type of error doesn’t seem to be discussed very much in the available information on freesurfer quality control as far as we’ve seen. Thanks in advance for any thoughts recommendations or advice you might be able to offer.
Best regards, Ben