For the mgz volumes, you should be able to do something like mri_add_xform_to_header -c /new/path/to/xfm brain.mgz
For the labels you could just use something like sed s/oldsubjectname/newsubjectname On 1/17/2020 3:48 AM, Tim Schäfer wrote: > External Email - Use Caution > > Hi Douglas, > > sure, you can get two example files here: > > wget http://rcmd.org/tmp/brain.mgz > wget http://rcmd.org/tmp/lh.BA1_exvivo.label > > The brain volume contains the ID because it stores the full path to the > tairach xfm (which includes the folder name, so the ID). You can check by: > > mri_info brain.mgz | grep talair > > (In this case the ID is 'tim'). > > Without mri_info, you can get it as well: > > mv brain.mgz brain.gz > gunzip -c brain.gz | strings | grep talair > > The second file is an ASCII label from the same subject. You can get the ID > by running: > > head -n 1 lh.BA1_exvivo.label > > There are some other files which contain the ID, these are just 2 examples. > > > I am currently in contact with the people running the consortium server and I > am not really sure whether the rule that the ID must not be in the files > makes any sense at all. Maybe I can get around this. > > > Best, > > Tim > > > > >> On January 17, 2020 at 12:23 AM "Greve, Douglas N.,Ph.D." >> <dgr...@mgh.harvard.edu> wrote: >> >> >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
