External Email - Use Caution

I find the recon-all table to be helpful:

http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0...

In this case, you probably need to run -autorecon2, as all subsequent steps are affected by the brainmask.mgz file.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Darko Komnenić komnenicd@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, November 30, 2020 at 12:49 PM To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] arguments to use after pial edits {Disarmed}

External Email - Use Caution 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. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1axQ4MDEpKp0YzmdtIT0FMnRvWx1u9q40rw_YBR1jd7UPMO...https://secure-web.cisco.com/134OA5xpyRuAJ4raLibeAZDGkJ8VFvtiCm69m7hXhYD4428DFSCfEHGfgqrFW8Iy9j3fJwoPH3RYxnGtC4RODybQrKIB7cYVEtiYb5Ht890ElcGU27h8UJTajTxw8bQM6DNX8uqRuTEsFMh720x4PCSoFbpcnXQ1qN-TcVNAFNAKkD81ND2J8smWHqWlI6qkxbWEjDiDRHI0m_qszNz9xnV1WceNN4uBMUUzCFu9IWx7lud9Ln0YGfV8xpSphDINNwS1qCvV2U95jfq_jYQLp_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEdits_freeview

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

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