Hi Bruce and Clara,

Thanks for your comments. Indeed the bright points are segmented as WM in wm.mgz, however these errors do not occur only in a few places but in many slices throughout the brain so manual edits will be quite extensive, which is why we wanted to double check that there is no parameter tweak to recon that might at least help some of these errors. But sounds like there's no way to adjust the parameters of recon to mitigate this type of error? If not we will move forward with manual edits to wm.mgz as you suggest. Thanks!

Best regards,
Ben

On Fri, Sep 2, 2016 at 8:36 AM, Clara Kühn <ckuehn@cbs.mpg.de> wrote:
Hello Ben,

I am no expert, I can only talk from my experience.
I've had similar images in my data. Those might be blood vessels or dura that were included in the surface. If they are included in the surface on more than 5 slices and pretty well visible you could delete those voxels from the brainmask. From the looks of the attached screenshots however I wouldn't worry about the brainmask but rather remove a few voxels from the wm.mgz. Then you rerun the subject with the -wm flag and check again. If it is only on one or two slices, though, I wouldn't edit it at all. The surfaces are just not going to be perfect.

Hope I could help.
Clara


----- Ursprüngliche Mail -----
Von: "Benjamin Baird" <benjamin.s.baird@gmail.com>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 1. September 2016 21:56:58
Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright        spots) in cortex

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 advice you might be able to offer.

Best regards,
Ben




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