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See also [[http://www.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI|MBIRN page]] |
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| Example: | * [[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. Use gunzip to decompress these downloads, ie.: |
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| mri_deface orig.mgz talairach_mixed_with_skull.gca face.gca orig_defaced.mgz | 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 |
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| 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. |
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.