The subcortical GM structures are obtained from the whole brain segmentation (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the label of the closest point on cortex (Salat, Neuroimage, 2009)

On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:

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Dear FreeSurfer experts,

I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean.

I would really appreciate some clarification. I am using FreeSurfer 7.1.1

Thanks in advance.

José

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