Automated Defacing Tools


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.:

gunzip mri_deface-v1.22-Linux64.gz
cp mri_deface-v1.22-Linux64.gz mri_deface
chmod a+x mri_deface
gunzip talairach_mixed_with_skull.gca.gz
gunzip face.gca.gz

Then, example usage, using the example input volume:

./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz

For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti:

./mri_deface my_T1.nii talairach_mixed_with_skull.gca face.gca my_T1_defaced.nii

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:



AutomatedDefacingTools (last edited 2016-06-08 15:12:36 by AllisonStevens)