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Dear FreeSurfer experts,
I have two questions on subject IDs in FreeSurfer output.
1) is it possible to change to subject identifier in the FreeSurfer output after recon-all has been run?
Background: I would like to upload data pre-processed with FreeSurfer to a consortium server. The subject ID is a random identifier, but the upload guidelines say this identifier must only occur in certain file types (Excel files, .log files, and some more, but not in any other files).
I noticed that a lot of the output files produced by FreeSurfer contain the subject identifier somewhere, including various binary files, so I guess there is no easy way to change it. But maybe there is? Like rerunning a part of recon-all?
2) If not, I could rename the source NIFTI files (e.g., from the identifiers to something like 'subject001', 'subject002', ...) and re-process everything. This would take some computational time for the > 500 subjects, but it would be okay I guess.
But a large number of the subjects have manual edits applied already. Is there a way to keep the manual edits? E.g., I thought maybe I could rename the individual directories of the edited subjects, leave the edited files in there, and run recon-all again. But what would happen? Will the new output files have the renamed ID from the directory name (and thus the recon-all command line), or will they still use the old ID (from the header of the existing files)? Or will the existing, edited files which contain a different ID be ignored during the new run because the IDs do not match, and thus the existing edits would have no effect?
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany