| Deletions are marked like this. | Additions are marked like this. |
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| * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/sample_T1_input|sample_T1_input.mgz]] - This is a sample input volume used in the example. Replace with your own input. | |
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| Then, example usage, using your orig.mgz: | Then, example usage, using the example input volume: |
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| ./mri_deface orig.mgz talairach_mixed_with_skull.gca face.gca orig_defaced.mgz | ./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz |
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| If you do not have the 'orig.mgz' file as input (which would only be the case if you have processed your data using the Freesurfer package), then just substitute the name of your T1-weighted input file, which can be a dicom or nifti: | For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti: |
Automated Defacing Tools
See also MBIRN page
Note: A license file is no longer necessary to use these tools:
sample_T1_input.mgz - This is a sample input volume used in the example. Replace with your own input.
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