Hi Steve I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want.
I don't have write permissions to that directory, but I'll see if I can get help to copy it. cheers Bruce On Wed, 29 May 2013, sle...@nmr.mgh.harvard.edu wrote: > The script mri_deface which is called by recon-all with the -deface flag, > requires the existence of two files > > /usr/local/freesurfer/stable5/average/face.gca > /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca > > The former exists where it should, the latter does not exist at that > location, although it can be downloaded from > > http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads > > and gunzipped. When I copy it into a directory and call mri_deface > directly, it works OK because it can find that image locally. But when I > call recon-all with the -deface flag, it looks for the file where it does > not exist, i.e. > > /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca > > Could someone with the appropriate permissions please copy that file to > where recon-all expects to find it? > > Second question: If I call recon-all with the -deface flag, does it deface > ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only > deface a copy of orig.mgz to orig_defaced.mgz? > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
