you can use mri_aparc2aseg. Look in the recon-all.log file of an individual for the command used to generate the wmparc.mgz.

On 08/01/2017 04:43 PM, Eryilmaz, H. Hamdi wrote:

Hi Anastasia and FS experts,

I am trying to create a white matter ROI mask underneath a cortical ROI label (e.g., 2 mm into the white matter) created in fsaverage space. I will then use this mask to extract values from individual dtifit_FA and dtifit_MD maps generated by trac-all. What would be the easiest way to do this? I thought about using mri_aparc2aseg but I am not quite sure about how to specify a label with this command.

Thanks so much for your help!

Best, Hamdi

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