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:
External Email - Use Caution
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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