You don't need the -legacy flag. Just make a copy of your v6 data and then run recon-all -all -s subject It will see and apply your previous edits.
On 9/22/2021 2:14 AM, Amanda Boyes wrote:
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Hi FreeSurfer experts,
Just checking whether anyone has any advice on my query below?
I would greatly appreciate any advice regarding how to incorporate masks/pial edited in v6 into the v7 pipeline.
Thanks and best wishes,
Amanda
*From:*Amanda Boyes *Sent:* Thursday, 16 September 2021 4:37 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Migrating data from v6 to v7
Hi fellow FreeSurfer users,
I am part of a longitudinal project and have a large dataset that has been processed in v6.
I have now upgraded to v7 and would like to update my processed data, retaining the existing manual masks and pial edits.
I found an old ReconAllChanges page (January 27, 2006, last updated 2012) referring to this as a “legacy data set” *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://freesurfer.net/fswiki/ReconAllChanges https://secure-web.cisco.com/1Xv4IBldXeMiwS_vnz2yxkzZjRrmjWqdrWlH8BEGlfzEpFPqPXDLTt6_VYouJsAyTcNDZs4uvp6WGpa53tOLQv4oqGDgRrc_6ZOWqwUnqeDjNsKpSqR2JW3BbQc0hcHoZdbA6J9JQcAUqQX7duVM57O-kRqFjGIYOuW5sP7LXL2vASdqald9XZYWRmCF09Fg244AiXgRByatGXfWucjEHbAxhl82VxtJi7EvOCG13n9dGlL22SjKZtm6AuaIXeVShRyoOaJuK-b42JDZhs-KfVw/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FReconAllChanges
I have also found a recon-all wiki page (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all https://secure-web.cisco.com/1nvZmuBoQ85ubAmAW6yY6sLfuFWqvMeZLmQkdE8XLYxKLANTO34WUP4l6EFUIofzOppjpYGGLpuGeW6ZVkDTwM_lh571b71ofitfz7vb0V9Im0coX464qBbbLQYgUWWfND_YaRs4Hf3Z98tlPwebXpTRhrN3jN9pRmdL-PVE0cLP-z8LIrs0AxVRTLn2YzuFujSDHTASEyhaLXdSJjgElOrWo4LDz0KmOBcka4-9NnkjPFHpMJOBQOesaTarO7gljW3T5NIHIYU06w9S_KC5GDA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all last updated 2017) suggesting the use of the following command for legacy datasets: recon-all -subject subjectname -all -legacy
Unfortunately, the -legacy flag is not recognised in v7.
I would be grateful for any advice on how to update my existing data from v6.0.0 to v7.2.
Thank you in advance,
Amanda
*Amanda Boyes*
/My pronouns are she/her/hers/
PhD Candidate and Research Assistant (Youth Mental Health) Thompson Institute
USC
Tel: +61 7 5456 3886
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