Dicom to Analyze

Dicom to analyze.img
Conversion of Dicom files into a analyze.img

Written by Owen Phillips. Email Dr. Katherine Narr if you have any questions. For more information, see the protocols page.


There are a couple of options for converting dicom data into a useable image format. For the Depression ECT project, use /ifs/woods/AIR/dicom2analyze and the script */narr/schizo/DEPRESSION/SCRIPTS/Processor.csh. For the Processor.csh script, you just need to change the subject ID within the foreach loop.

Siemenstoanalyze.jar file.

  1. Download Siemens to analyze.jar.
  2. You can run SiemensToAnalyze.jar locally or on qsub.loni.ucla.edu or cerebro-dev-0.loni.ucla.edu.
  3. First ssh -X username@qsub.loni.ucla.edu
  4. /usr/java2v14/bin/java -Xmx400000000 -jar SiemensToAnalyze.jar -recursive -target analyze_source -input [directory]
  5. Note, if you are part of the Narr group, you don't have to download the .jar file. Instead use, ~narr/SiemensToAnalyze.jar