Diff for "AutomatedDefacingTools"

Differences between revisions 1 and 5 (spanning 4 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

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 your orig.mgz:

./mri_deface orig.mgz talairach_mixed_with_skull.gca face.gca orig_defaced.mgz

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:

./mri_deface my_T1.nii talairach_mixed_with_skull.gca face.gca my_T1_defaced.nii

-  ⇤ ← Revision 1 as of 2009-07-22 19:01:49 → 
  Size: 831
  Editor: NickSchmansky
  Comment:
+   ← Revision 5 as of 2013-02-19 12:11:57 → ⇥
  Size: 1514
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
+See also [[http://www.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI|MBIRN page]]
-Line 10:
+Line 12:
-Example:
+Use gunzip to decompress these downloads, ie.:
-Line 12:
+Line 14:
-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
-Line 14:
+Line 20:
+Then, example usage, using your orig.mgz:
{{{
./mri_deface orig.mgz talairach_mixed_with_skull.gca face.gca orig_defaced.mgz
}}}

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:
{{{
./mri_deface my_T1.nii talairach_mixed_with_skull.gca face.gca my_T1_defaced.nii
}}}