Transferring Data from the Scanner and Converting it to Analyze Format

The short version:

The full version:

To transfer data from the scanner to the ALBMC server electronically, you need to have an assigned group name. All group names must consist of at least 8 uppercase letters and the first 8 letters must be unique. This format allows DICOM processing software, which expects this convention to be followed, to be used without modification. For illustrative purposes, the name SOMEDICOMGROUP will be used here, but should be substituted by a group name assigned to your project.

To transfer data:

  1. When you register the subject for scanning, enter your group identifier (e.g., SOMEDICOMGROUP) into the Referring Physician field on the scanner patient registration page
  2. You do not need to do anything to transfer the data from the scanner to dns0; this transfer will happen automatically.
  3. After transfer, to access the data from a generic networked computer, connect the the ALBMC server (dns0.bmap.ucla.edu) using ssh. For data collected before April 1, 2008, it will be located in a subdirectory of /Volumes/BMC1/dicom/. For data collected on or after April 1, 2008, it will be located in a subdirectory of /Volumes/BMC5/dicom2/. The subdirectory will match the group name that you provided in the Referring Physician field (e.g., the subdirectory 'SOMEDICOMGROUP' for the group 'SOMEDICOMGROUP'). Only members of the specified group (as defined on the server) will be able to access data within a particular group directory.
  4. If you are working on a Macintosh computer in the ALBMC, detailed instructions for navigating to your data without using ssh are provided.
  5. The files will have been pre-sorted into folders based on acquisition date, then subject name, then Study ID, then Series Number.

NOTE: The directories to which the DICOM files are transferred are read-only. You cannot create new files within these directories.

To convert DICOM data into Analyze format data using the command line version of LONI Debabeler:

  1. Make sure you have Java 1.4 or later installed on your machine (on Mac OS X, type 'java', on other UNIX machines, type '/usr/java/bin/java' to see the current version number)
  2. Open a command line terminal and set the working directory (e.g by using the 'cd' command) to the directory in which you want the converted images to be placed (you must have write permission in this directory)
  3. Identify a pathname to the converter SiemensToAnalyze.jar. For example, if you keep the converter on your Mac OS X Desktop, you could use ~/Desktop/SiemensToAnalyze.jar
  4. Identify pathnames to all the files you want to convert. For example, to convert all the files collected on October 07, 2007, you might use /Volumes/BMC1/dicom/SOMEDICOMGROUP/20071007/*/*/*/*
  5. Identify the pathname to java on your computer (on Mac OS X, this is simply 'java', on most other UNIX machines, it is '/usr/java/bin/java')
  6. Execute the command: {PATHNAME_TO_JAVA} -Xmx200000000 -jar {PATHNAME_TO_SIEMENS_TO_ANALYZE_DOT_JAR} -target analyze_source -input {PATHNAME_TO_INPUT_DICOM_FILES}
  7. On Mac OS X, this command might look like 'java -Xmx200000000 -jar ~/Desktop/SiemensToAnalyze.jar -target analyze_source -input /Volumes/BMC1/dicom/SOMEDICOMGROUP/20071007/*/*/*/*
  8. On the datalab computers, an abbreviated command can be used: SiemensToAnalyze {PATHNAME_TO_INPUT_DICOM_FILES}
  9. This abbreviated command would look like 'SiemensToAnalyze /Network/Servers/BMC1/dicom/SOMEDICOMGROUP/20071007/*/*/*/*
  10. After conversion, the converted output files will be sorted into subdirectories inthe directory from which the conversion command was invoked. The data will be sorted first by subject name, then by Study Description (with date and time appended), then by Series Description (with date and time appended)

The converter should do all of the following by design:

If you want to copy the SiemensToAnalyze.jar file from the server to your local machine, it is stored in /Volumes/BMC0/BMCUsers/imaging_tools/Debabeler/. On the datalab machines, you can find it in /Network/Applications/Debabeler.

Updated December 13, 2013