Diff for "AutomatedDefacingTools"

Differences between revisions 4 and 6 (spanning 2 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

-  ⇤ ← Revision 4 as of 2013-02-19 11:26:58 → 
  Size: 1185
  Editor: NickSchmansky
  Comment:
+   ← Revision 6 as of 2013-02-19 12:21:40 → ⇥
  Size: 1597
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 12:
+ * [[https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/sample_T1_input|sample_T1_input.mgz]] - This is a sample input volume used in the example.  Replace with your own input.
-Line 20:
+Line 21:
-Then, example usage, using your orig.mgz:
+Then, example usage, using the example input volume:
-Line 22:
+Line 23:
-./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 24:
+Line 25:
+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
}}}