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| ## page was renamed from Automated Defacing Tools ## page was renamed from mri_deface |
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| [[https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace|See MiDeFace]] |
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| Cite this paper is using mri_deface: [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408762/|A Technique for the Deidentification of Structural Brain MR Images]] |
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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 |
mv mri_deface_linux mri_deface |
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| Then, example usage, using the example input volume: | The command usage is: |
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| ./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz | ./mri_deface <input> talairach_mixed_with_skull.gca face.gca <output> |
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| For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti: | So as an example, to deface your T1-weighted input file, which can be a dicom or nifti, run: |
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| ./mri_deface my_T1.nii talairach_mixed_with_skull.gca face.gca my_T1_defaced.nii | ./mri_deface T1.nii.gz talairach_mixed_with_skull.gca face.gca T1_defaced.nii.gz |
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| 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. | 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. [[http://www.mccauslandcenter.sc.edu/mricro/mricron/|MRIcron]] is a good option (use MRIcron, not MRIcro, because you will want nifti support). |
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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.:
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:
