Mbirn deface: starting from dicom images

• Convert DICOM to AFNI BRIK

  to3d <dicom images>

This will bring up a GUI in which the user must specify image orientation and filename to save. Use to3d -help to see how to automate this from the command line.

• run mri_deface:

  mri_deface myInput+orig.BRIK $FREESURFER_DIR/average/talairach_mixed_with_skull.gca $FREESURFER_DIR/average/face.gca defaced.mgh

where myInput+orig.BRIK is the file for which we create a mask, and defaced.mgh is the created mask.

• run mri_mask:

  mri_mask myInput+orig.BRIK defaced.mgh myOutput.img

where myInput+orig.BRIK is the file to be masked, defaced.mgh is the mask we created in the previous step, and myOutput.img is the output image

• if necessary, convert the myOutput.[hdr/img] to your favorite format for viewing