if there are both use -autorecon2-wm -autorecon3. There is also the option of adding control points and running -autorecon2-cp -autorecon3

cheers Bruce On Thu, 1 Aug 2013, Stéphane Poulin wrote:

Dear Freesurfer experts, Regarding recon-all troubleshooting, my understanding is that you can edit wm and complete the pipeline with recon-all –autorecon2-wm. Similarly you can complete the pipeline with recon-all –autorecon2-pial if there is a problem with the pial surface. If there are both white matter and pial surface edits, is there an “efficient” way to correct for both and complete the pipeline. Thanks, Stephane

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