First you need to get an annotation/parcellation of the lobes. You can try using mri_annotation2label with the --lobesStrict; it may or may not correspond to what you consider lobes to be. Next you need to run mri_aparc2aseg specifying your lobes annotation. Look in the recon-all.log file for an example of the command that creates the wmparc.mgz and modify the command to reference your lobes annotation (specify a different output). You will need to create a new look up table to include your WM lobes segmentation (see FreeSurferColorLUT.txt)

On 09/29/2016 12:31 AM, Zhiliang Long wrote:

Dear freesurfer experts:

I was wondering if it would be possible to parcellate whole white 

matter into different lobules (e.g. white matter in frontal lobule, parietal lobule, temporal lobule, and so on) by using Freesurfer ? My goal is to compute the white matter volume, as well as FA wihtin different lobules.

Best,

Zhiliang

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