Hi Tim

you probably also want to do the files in the orig dir (like orig/001.mgz).

cheers Bruce On Fri, 27 Sep 2019, Tim Schäfer wrote:

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Dear FS experts,

I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium server, and they require all data to be anonymized.

I found mri_deface [1] and wondered which files I would have to apply it to, and whether there are any other things I should be aware of.

So far, my plan is to use mri_deface to replace, for each subject, the following files in mri/:

• orig.mgz
• orig_nu.mgz
• T1.mgz
• rawavg.mgz

It would also be an option to upload only a subset of all the files produced by FreeSurfer, but I do not know which files to exclude and include, so if you have suggestions for this, it would also be very welcome. I will also look at some public datasets to see how they did it.

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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