https://www.na-mic.org/w/index.php?action=history&feed=atom&title=Mbirn_deface%3A_starting_from_dicom_imagesMbirn deface: starting from dicom images - Revision history2026-05-04T10:52:42ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Mbirn_deface:_starting_from_dicom_images&diff=3558&oldid=prevAndy: Update from Wiki2006-12-18T13:25:01Z<p>Update from Wiki</p>
<p><b>New page</b></p><div>* Convert DICOM to AFNI BRIK<br />
<br />
to3d <dicom images><br />
<br />
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.<br />
<br />
* run mri_deface:<br />
<br />
mri_deface myInput+orig.BRIK $FREESURFER_DIR/average/talairach_mixed_with_skull.gca $FREESURFER_DIR/average/face.gca defaced.mgh<br />
<br />
where myInput+orig.BRIK is the file for which we create a mask, and defaced.mgh is the created mask.<br />
<br />
* run mri_mask:<br />
<br />
mri_mask myInput+orig.BRIK defaced.mgh myOutput.img<br />
<br />
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<br />
<br />
* if necessary, convert the myOutput.[hdr/img] to your favorite format for viewing</div>Andy