BIRNDUP at NMR

• Make sure that /usr/java/j2sdk/bin is in your path so that you can run java. which java should return /usr/java/j2sdk/bin/java.
• cd ~nicole/work/slicer2
• ./slicer2-linux-x86
• Click on More
• Click on BIRNDUP
• Click on Run Interface
• Click on File->Preferences and set the following values:
  • DCANON_DIR /autofs/space/birn_045/users/BWH/nicole/anonym_scripts/dcanon
  • DEFACE_DIR /autofs/space/birn_045/users/BWH/nicole/deface
  • LINKTABLE /autofs/space/birn_045/users/BWH/nicole/deface/linktable
  • UPLOAD2_DIR /autofs/space/birn_045/users/BWH/nicole/upload2
• Select directory that has a DICOM volume in it
• Set project, visit, study numbers
• Set drop down to Deface
• Click Sort
• Click Deidentify for the volume's new id
• New slicer pops up with a movie showing the defacing if all goes well, defaced dicom is in

${DEFACE_DIR}/Project_[projectnum]/[new id]/Visit_[visitnum]/Study_[studynum]/Raw_Data/[volume]-anon/Deface