Diff for "AutomatedDefacingTools"

Differences between revisions 2 and 11 (spanning 9 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.

Sample input before and after defacing:

-  ⇤ ← Revision 2 as of 2011-02-10 10:38:32 → 
  Size: 1085
  Editor: NickSchmansky
  Comment:
+   ← Revision 11 as of 2013-02-19 12:41:47 → ⇥
  Size: 1925
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
+See also [[http://www.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI|MBIRN page]]
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+Line 7:
-Line 10:
+Line 13:
+ * [[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.
-Line 11:
+Line 16:
-Line 18:
+Line 24:
-Then, example usage, using your orig.mgz:
+Then, example usage, using the example input volume:
-Line 20:
+Line 27:
-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
-Line 22:
+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.

Sample input before and after defacing:
{{attachment:sample_T1_input.jpg}}
{{attachment:sample_T1_input_defaced.jpg}}