External Email - Use Caution Thank you so much! This was very helpful. I did not know that the command will respect my edits. For some reason, this did not happen for one of the subjects, and it looked like that the command completely regenerated the base. But it worked when I tried again with a different subject.
All the best, Eszter Boros Douglas N. Greve <dgr...@mgh.harvard.edu> ezt írta (időpont: 2021. aug. 18., Sze, 22:06): > That command will re-run the base, but it should respect your edits. Is > that not the case? If you just want to re-run part of it, you can specify > the stage (eg, -autorecon2) instead of -all > > On 8/18/2021 8:05 PM, Eszter Boros wrote: > > External Email - Use Caution > Thank you for your answer! > > I think I should clarify this question a little bit. > So this is about correcting the Base. And run recon-all *after *correcting > the Base. > What command should I use here? if I want to regenerate only the Base > after correcting it? > > Because the common below does not work: (ERROR: must specify subjects for > base subject using -base-tp) > recon-all -base OAS2_0057 -autorecon-pial > > But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp > OAS2_0001_MR2 -all" > that just creates a new Base based on the cross MR1 and MR2. > > My question is how can I regenerate the corrected Base? What command > should I use? > > Thank you so much! > > All the best, > Eszter Boros > > > > > Eszter Boros <boros.eszter0...@gmail.com> ezt írta (időpont: 2021. aug. > 8., V, 19:04): > >> Dear FreeSurfer Team, >> >> I am working on a longitudinal pipeline and after correcting the Cross >> and generating the Base, I can still see some pial problems sometimes (on >> the Base). >> >> I read on the Freesurfer website that it is possible to correct and >> regenerate only the Base, but when I use this command: >> >> recon-all -base OAS2_0057 -autorecon-pial >> >> /where OAS2_0057 is the name of the Base/ >> >> I get the following error message: >> >> ERROR: must specify subjects for base subject using -base-tp >> >> >> Why is this not working? I am using Freesurefer 7.1.1. >> >> Thank you so much! >> >> All the best, >> Eszter Boros >> >> > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1anCg8GNKI3yfzO10dKE83C29u6BsodpytJidG9dSNveD6YucSTHUp_cjBkgGzarrtZ4v7iWaZxC5EwZIdJB8KXuHyudZvDT9kOLMloJWOPOgYkLTOwnCZLzRHK7dyn_sixU4Kmo_ELwYUIPZVXmUuhsKt7nitc3K8OfdyqvtC93sVtQ-qwYboOoDOBHXELh6Fd1zeaFSfsDHNKNsj7LZfu3muioj374MVtG1o2W2raWndih6_DmmwCqPvfoBzt0NKmxKHjjzQT2SwNwqm_K4dw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1x-jbqfmrQUW-E0zZTkVPtzKDYwj0fM_inLixBO2uS-Rg6i6yCTTZWJ40s2hZPAVg3t9Mx96KIXEUd0dkUg-nWBLZLwzoB36jzskEbkxTpFmzdGuaBaUlcnbQexJ5JKURFSLBQRp5y3wMtVOQ7nq_XvbB2V4BL-jwzbEl9JkywzuLcTk4BsvcS3nIr_TcXIFVKdiyRxyxFpvJo75VqyVVsBdHqs4P8afotiCIL6-_V9BbnA4jrQEQ8IH5h4IosHMfNhPf4IvJz5CXANkTrqEJVg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. >
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