Diff for "AutomatedDefacingTools"

Differences between revisions 2 and 13 (spanning 11 versions)

Automated Defacing Tools

Note: A license file is no longer necessary to use these tools:

mri_deface v1.22 for Linux 64bit
mri_deface v1.22 for Linux
mri_deface v1.22 for Mac OSX Leopard Intel
talairach_mixed_with_skull.gca
face.gca
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. MRIcron is a good option (use MRIcron, not MRIcro, because you will want nifti support).

Sample input before and after defacing:

-  ⇤ ← Revision 2 as of 2011-02-10 10:38:32 → 
  Size: 1085
  Editor: NickSchmansky
  Comment:
+   ← Revision 13 as of 2013-02-19 18:59:32 → ⇥
  Size: 2074
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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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+ * [[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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-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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+Line 29:
+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.  [[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}}