This package sets up a DICOM image reconstruction server. It is able to:

• Listen to and handle incoming DICOM transfer
• Process the incoming DICOM image with customized reconsturction script
• Push the processed DICOM image back to the request peer.
• Back up all the DICOM transfer history to a external storage device on a daily basis.

• System: (tested on)

  • Ubuntu 14.04 LTS 64bit
  • Ubuntu 15.10 64bit
  • Mac OS X 10.6.8
  • Mac OS X 10.10

• Software:

  • daemonize
  • dcmtk 3.6.0

• Reconstruction script:

  This package uses program "medin" for DICOM --> QSM reconstruction.

  However, it can be replaced by any command-line reconstruction script whose input/output format is DICOM image, with changes in auto_QSM/src/recon_script accordingly.

1. Unzip the package:

   $ tar -xvzf auto_QSM.tar.gz
   

   or get it from Github:

   $ git clone https://github.com/leonhart217/auto_QSM.git
   

2. cd to the root folder:

   $ cd auto_QSM
   

3. Prepare binary files with auto_QSM/dep/bin_dep_[Your System Version].tar.gz:

   $ mkdir -p bin
   $ tar -C bin -xvzf dep/bin_dep_[Your System Version].tar.gz
   

   [Note]: if your OS is differnet from those in Requirement, you may need to compile/install the required dependency binary file from source code:

   • average_binary:

     Source code: auto_QSM/dep/src_dep.tar.gz/average_binary.c

   • storescp_mod:

     Source code: auto_QSM/dep/src_dep.tar.gz/storescp_mod.cc

     Compiled with dcmtk 3.6.0

   • gdcmdump:

     Install GDCM 2.4

4. (Optional) Add auto_QSM/bin to $PATH in order to debug the package from command line

   For example for Ubuntu:

    $ echo "export PATH=\$PATH:$(pwd)/bin" >> ~/.profile
    $ . ~/.profile
   

   or for Mac OS X:

    $ echo "export PATH=\$PATH:$(pwd)/bin" >> ~/.bash_profile 
    $ . ~/.bash_profile
   

5. run

    $ ./install
   

• System setting: auto_QSM/src/setup_config

  • disk_data_fix:

    This is recommended to be manually set for the Filesystem of server's system drive ${disk_data}

• User setting: auto_QSM/etc/config_user

  • flag_auto_backup:

    Automatically backup data from DICOM archive in system drive to external drive. Backup will happen when available space on ${disk_data} is below 80GB, and only happen at 3am ~ 5am, at most once per day.

    [Note]: if this option is on, it is recommended to manually set ${mount_backup_fix} in auto_QSM/src/setup_config.

• Scanning list: auto_QSM/etc/scanner_list

  Information of new scanner should be added as a row with:

    [manufactor brand]	[AETitle] [IP address] [port] [relay server name, if needed]
  

• If any configuration changes are made, restart the server by (Make sure the server is not currently running anything important):

    $ auto_QSM/src/restart_all
  

• Q1: Do I need to compile the dcmtk and daemonize before installing this package?

  A1: Compilation and installation of dcmtk and daemonize are recommended. However, one can choose to use pre-compiled binaries for dcmtk which is available online here. For pre-compiled binary for daemonize, please contact the author.

  [Note]: when using pre-compiled binaries, please make sure the path to the binaries is added to $PATH in crontab.

• Q2: How do I check if the package is properly functioning?

  A2: Simple check: in Ubuntu or Mac OS, run:

    $ ps -u ${USER} -f | grep auto_QSM
  

  Typical output has one running instance for each of "qsmrecon_main", "dicom_listen" and "check_log_size". It also has one or more instances for "storescp_mod". If flag_auto_backup is on, it should also has one instance of "auto_backup".

  Full check: more detailed information can be found in the log files:

  buffer/log_stdout_qsmrecon_main: log of the recon script (E.g. check if one series is completely received; archive received DICOM; examine the DICOM header information).

  buffer/log_stdout_dicom_listen: log of DICOM transfer (E.g. check if a port has been used; check if a peer is able to be accessed).

  buffer/log_QSM: log of successfully reconstructed case(s).

• Q3: How do I un-install this package?

  A3:

  1. Backup the data in your DICOM archive ($HOME/data by default)

  2. Run (under auto_QSM)

     $ cat crontab.bak | crontab -
     $ src/kill_all
     

  3. Remove the auto_QSM folder

For further questions, please contact the author

• Email: [email protected]