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Dear Freesurfer experts, I am using Human Connectone Project pipelines to calculate cortical myelin levels. These pipelines use Freesurfer 6. Since certain subjects' brain surfaces had some chunks and spikes sticking out, I edited the brainmask.mgz file for those subjects as described in this tutorial. https://secure-web.cisco.com/134OA5xpyRuAJ4raLibeAZDGkJ8VFvtiCm69m7hXhYD4428...
To get the myelin maps again, I got the instruction from the HCP mailing list that I should call again the FreeSurferPipeline script, but add the --existing-subject and --extra-reconall-arg flags. If I understood correctly, after --extra-reconall-arg flag, there should be an equal sign, and then keywords that specify which recon-all stages I want to run.
Could you please tell me what those stages are, i.e. what keywords I should use after the equal sign? I want to keep the brainmask.mgz file that I edited, and then repeat all the steps that happen after braimask.mgz is generated. I was referred to the FS tutorials/wiki at the HCP mailing list, but I would like to double-check with someone here. Based on the tutorial link above, it seems this should be "-autorecon-pial -subjid pial_edits_before", but I'm not sure if this would be applicable in this case.
Thanks in advance and I hope my question wasn't too confusing. Best, Darko