Diff for "AutomatedDefacingTools"

Differences between revisions 7 and 21 (spanning 14 versions)

Automated Defacing Tools

See MiDeFace, our newest tool for defacing

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:

-  ⇤ ← Revision 7 as of 2013-02-19 12:22:11 → 
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+   ← Revision 21 as of 2022-08-05 14:31:35 → ⇥
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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, our newest tool for defacing]]
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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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+Line 37:
-./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.  [[http://www.mccauslandcenter.sc.edu/mricro/mricron/|MRIcron]] is a good option (use MRIcron, not MRIcro, because you will want nifti support).

Sample input before and after defacing:

{{attachment:sample_T1_input.jpg}}

{{attachment:sample_T1_input_defaced.jpg}}