Accessing DICOM Data


How to Retrieve Dicom Data from the Brain Mapping Center

Useful Links

• Accessing DICOM data from the data lab computers

• BMC Tech Line: (424) 652-6290

• Email BMC Techs

 

1.     If you are outside of the Brain Mapping Center building you will need to connect to BMC via VPN

·        If you do not have a VPN client, you can download and install it here: https://www.bol.ucla.edu/services/vpn/

·        Once you install the program, change the server name to “vpn.bmap.ucla.edu”  

·        Enter your BMC Network account username and password

 

2.     Connect to the BMC network dicom server

·        If you using a MAC computer:  

o   Click go/connect to server (shortcut key:    )

o   Enter the server address: afp://dns0.bmap.ucla.edu or afp://164.67.4.100  

o   Log on with your network account credentials

·        If you are using a Windows computer:  

o   Open "File Explorer" and then open  “Map Network Drive”

o   In the folder field type:  \\164.67.4.100\dicom6\ (or whatever dicom group you would like to access)  

o   A security window will pop up asking for your BMC network account credentials

 

3.     After inputting your username and password you will see a list of groups

·        You will only be able to access approved Group folder(s)

·        If you need access to a Group folder please email James Widanta (jwidanta@ucla.edu) to request a network access form

·        The groups PIs must sign the form to approve access

 

4.  Dicom Data Storage Directories: 

·        DICOM data collected before Tuesday, April 1, 2008 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC1/dicom/

·        DICOM data collected on or after Tuesday, April 1, 2008 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC5/dicom2/

·        DICOM data collected on or after Thursday, April 1, 2010 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC8/dicom3/

·        DICOM data collected on or after Sunday, January 1, 2012 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC9/dicom4/

·        DICOM data collected on or after Thursday, June 12, 2014 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC9/dicom5/

·        DICOM data collected on or after Monday, May 16, 2016 is stored on dns0.bmap.ucla.edu in subdirectories of /Volumes/BMC9/dicom6/

 

Transferring Data from the Scanner 

 

To transfer data from the scanner to the ALBMC server electronically, you need to have an assigned group name. If you do not alreay have one, please contact James Widanta (jwidanta@ucla.edu) to have a GROUP name created.  DO NOT create your own group name on the scanner. 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.

  1. When you register the subject for scanning in the Scanner Registration page, use the drop-down arrow in the “Referring Physician” field to select your groups identifier (e.g. SMITH GROUP)."
  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.

Converting Data to Analyze Format

 

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 in the 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:

  • automatically detect and handle Siemens mosaic format images
  • convert all images (even single slice sagittals) to transverse format in the SPM (i.e., not-truly-Analyze compliant) neurological orientation
  • set the header maximum field correctly
  • correctly set the image dimensions and voxel sizes
  • create 3D Analyze format output files with time series files numbered sequentially starting with 1 and left padded

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 May 14, 2015