| Deletions are marked like this. | Additions are marked like this. |
| Line 7: | Line 7: |
| Line 13: | Line 14: |
| Line 14: | Line 16: |
| Line 22: | Line 25: |
| Line 25: | Line 29: |
| For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti: | |
| Line 26: | Line 31: |
| For your own data, substitute the name of your T1-weighted input file, which can be a dicom or nifti: | |
| Line 30: | Line 34: |
| Line 32: | Line 35: |
|
{{attachment:sample_T1_input.jpg}} {{attachment:sample_T1_input_defaced.jpg}} |
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
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. 
