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| [[https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace|See MiDeFace, our newest tool for defacing]] |
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| gunzip mri_deface_linux.gz | |
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| Then, example usage, substitute the name of your T1-weighted input file, which can be a dicom or nifti: | The command usage is: |
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| ./mri_deface T1.nii talairach_mixed_with_skull.gca face.gca T1_defaced.nii | ./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 |
Automated Defacing Tools
See MiDeFace, our newest tool for defacing
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:
