Please ignore my previous question - but I have a new one.

I have edited the base scans, making brainmask and finalsurfs.manedit edits and trying to rerun them. Now I am following https://secure-web.cisco.com/1VyAGi5WMbNSwIbrIdy7ORhoOoHjz-GgyeA9BhOoD_ruZYV... to reprocess the base so that recon-all will register my edits.

So my SUBJECTS_DIR has the cross sectional scans (which I haven't edited) and the edited base scans, and I run:

recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -autorecon2 -autorecon3

?but it errors, saying that it thinks the <templateid> I put is a cross-sectional scan (which it probably thinks so because its in SUBJECTS_DIR). What should I do to fix this?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Sent: Sunday, December 27, 2020 2:32 PM To: Freesurfer support list Subject: [External] [Freesurfer] FS longitudinal editing help {Disarmed}

Hi FS developers,

I am following the instructions based on: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1VyAGi5WMbNSwIbrIdy7ORhoOoHjz-GgyeA9BhOoD_ruZYV...https://secure-web.cisco.com/1VrFl1mbEYWyi1x-UM_ckT-4OJTESMrysix8j75yGcvVCwFdH67i_yLUC5tz7YrP5hXoNh15zJ81gfZ4A7_ZvYz1depxOgqRrRkxInt0E-_k3peD9XKx0XFzce8iBiADzxRmqEPMrjSpoSK7LQpAz72cpjWFTkCVLSS45m5eLhMxT4C2SPGgM-8GrUIuHydPOcdp-clbYxlqRiZ68BjgXJtXdDrmWGhVi6i7Md565JoVB7PWFkMd6aPcnJqSdiwg9VIYVEyRDlUtC9DdnHR5TCA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1R-_BDytOj92bKEInOUa5egJ0tPFR48r8ux5GKBDt1aqhf6eG1cPWej1-vHUXcwu1nsCjZVgl9-MpKEN5EvlwyRyZebsae_zlAoeB3Ivt5seF7OEU0zfzDcd03q9ycMfN9Tqwr4wxrAmkHD7W0tBKonzBuk5SifnaKvIwDQX7eCCd6fMJOO2FQHjHP1v7GLs__2r0fCN546Wl0mfQ99khejlyIC6XC3lYb6RMINIAAH97o2ZlTO2bqh6nDiJFUS1KKiefNCSOfBcdm_8pBWE4gQ%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FLongitudinalEdits__%3BJSUlJSU%21%21CvMGjuU%21u_LVCcL_ECYK9Hs0G68WwC-y5uLhCFhg7ZUSSZAZWO3mSMKsk18sHMdC269pmw-d5XZHNQ%24

I have run the longitudinal pipeline after meticulously editing the cross sectional scans, but see that after quality checking the base and follow up scans, the scans for the base and the longitudinal have their pial and white lines incorrect, as if I never edited the cross sectional scans. Am I right to observe this? Is it appropriate to register the qc'd brainmask/brain.finalsurfs.manedit.mgz from cross sectional to base/longitudinal, and why isn't this done already?

I am using FS6dev.

Thanks,

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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