In order to protect the privacy of your participants’ scans, we request that you submit only defaced and fully deidentified scans for processing by fsurf. Scans can be anonymized and deidentified before they are uploaded to OSG servers as described in this article.

You should use a local FreeSurfer installation to prepare your scans. First, on your local machine import your scan into FreeSurfer by running

  $ recon-all -subject SUBJECT -i PATH_TO_MGZ_INPUT_FILE

Here, recon-all is the FreeSurfer command line tool, the argument SUBJECT is the name of the subject, and the argument PATH_TO_MGZ_INPUT_FILE is the full path to the input file. The above command produces a single compressed image file 001.mgz under the directory subjects/SUBJECT/mri/orig. Now use mri_deface to deface the image as follows,

  $ cd  ${FREESURFER_HOME}/average
  $ mri_deface ../subjects/SUBJECT/mri/orig/001.mgz  \
               talairach_mixed_with_skull.gca  face.gca \

If the mri_deface program cannot find the needed *.gca files (the standard FreeSurfer parameter files), fetch and unzip them:

 $ cd ${FREESURFER_HOME}/average
 $ wget ""
 $ wget ""


This page was updated on Nov 12, 2019 at 09:45 from examples/FsurfRemote/