My guess is that this is a problem with the bias field correction. You can try putting in control points in to the WM around those areas (make sure they are fully in WM). From an automatic perspective, you could try running your own bias field correction and then pass that to recon-all. Eg, you could run something like
samseg --i inputvol.mgz --o samseg
This will create a samseg folder with a bias field corrected volume. Visualize that to make sure nothing bad happened, then pass that to recon-all

On 11/14/2024 6:17 PM, Boa Sorte Silva, Narlon wrote:

Hi there,
Hope all is well

Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration.

Nárlon Cássio

Nárlon C Boa Sorte Silva, PhD (He, Him, His)
Postdoctoral Fellow
Centre for Aging SMART, Vancouver Coastal Health Research Institute
Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute
Department of Physical Therapy, University of British Columbia

+15196944893

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