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 whitematter 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer