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 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface-v1.22-Linux64.gz|mri_deface v1.22 for Linux 64bit]]
 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface-v1.22-Linux.gz|mri_deface v1.22 for Linux]]
 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface-v1.22-MacOS-Leopard-intel.gz|mri_deface v1.22 for Mac OSX Leopard Intel]]
 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface_linux|mri_deface v1.22 for Linux]]
 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface_osx|mri_deface v1.22 for Mac OS]]
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 * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/sample_T1_input.mgz|sample_T1_input.mgz]] - This is a sample input volume used in the example. Replace with your own input.
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gunzip mri_deface-v1.22-Linux64.gz
cp mri_deface-v1.22-Linux64.gz mri_deface
gunzip mri_deface_linux.gz
mv mri_deface_linux mri_deface
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Then, example usage, using the example input volume:
Then, example usage, substitute the name of your T1-weighted input file, which can be a dicom or nifti:
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./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz ./mri_deface T1.nii talairach_mixed_with_skull.gca face.gca T1_defaced.nii
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For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti:
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{{{
./mri_deface my_T1.nii talairach_mixed_with_skull.gca face.gca my_T1_defaced.nii
}}}

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.:

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

Then, example usage, substitute the name of your T1-weighted input file, which can be a dicom or nifti:

./mri_deface T1.nii talairach_mixed_with_skull.gca face.gca 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:

sample_T1_input.jpg

sample_T1_input_defaced.jpg

AutomatedDefacingTools (last edited 2022-08-05 14:31:35 by DougGreve)