Automated Defacing Tools

defacing_figure.jpg

See also MBIRN page

Cite this paper is using mri_deface: A Technique for the Deidentification of Structural Brain MR Images

Note: A license file is no longer necessary to use these tools:

Use gunzip to decompress these downloads, ie.:

mv mri_deface_linux mri_deface
chmod a+x mri_deface
gunzip talairach_mixed_with_skull.gca.gz
gunzip face.gca.gz

The command usage is:

./mri_deface <input> talairach_mixed_with_skull.gca face.gca <output>

So as an example, to deface your T1-weighted input file, which can be a dicom or nifti, run:

./mri_deface T1.nii.gz talairach_mixed_with_skull.gca face.gca T1_defaced.nii.gz

You will need a volume viewer to view the resulting defaced file. The freesurfer package includes the 'freeview' viewer, but there are many others capable of reading dicom and nifti volumes. MRIcron is a good option (use MRIcron, not MRIcro, because you will want nifti support).

Sample input before and after defacing:

sample_T1_input.jpg

sample_T1_input_defaced.jpg

AutomatedDefacingTools (last edited 2020-03-25 14:34:07 by AndrewHoopes)