BIRNDUP at NMR

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  • 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