[Freesurfer] Hand Segmenting White and Pial Layers

Hi Freesurfer,

Here at I-LABS we just finished making a couple new 6-month and 12-month infant templates for ourselves and the neuroscience community to use.

When I run the template through the recon-all pipeline, there is significant blurring of the template as opposed to when I look at the original in FSL and the segmentation is not usable for our MEG source localization.

I would like to create the grey matter and white matter masks completely by hand over the next week or two from the original nifti image, and then have freesurfer use those masks in the surface reconstructions. Is this possible? If so, how can I do it?

Thanks so much in advance, Liv