Hi Tim, can you send a list of files that have the identifier. For volumes and surfaces, it might be as easy as running mri_convert/mris_convert using the same file as input and output.
On 1/13/2020 5:54 AM, Tim Schäfer wrote: > External Email - Use Caution > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
