The set of scripts that preprocess and insert MRI data into the database.
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mincpik

README.md

This Readme covers release 17.0 of the LORIS Imaging Insertion Pipeline for Ubuntu or CentOS systems

This repo accompanies the LORIS neuroimaging data platform main repo, release 17.0.*.
For documentation and detailed setup information, please see the LORIS wiki.

This repo can be installed on either the same VM as the main LORIS codebase, or on a different machine such as a designated fileserver where large imaging filesets are to be stored.

System Requirements

  • Perl
  • MINC toolkit (step 3)
  • DICOM toolkit (step 4)

On Ubuntu, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will apt-get install dcmtk.

For CentOS: Dependency installation notes are included in the LORIS wiki Imaging Setup page, Section 1 (installing codebase). As of the release date, this includes a transcript for CentOS installation and notes on dependencies including DICOM toolkit.

The following installation should be run by the $lorisadmin user. sudo permission is required. See aces/Loris README.md for further information and Loris installation information.

Installation

  1. Create directories and download Loris-MRI code

    sudo mkdir -p /data/$projectname/bin/mri
    sudo chown -R lorisadmin:lorisadmin /data/$projectname
    cd /data/$projectname/bin
    git clone -b master https://github.com/aces/Loris-MRI.git mri
  2. Install dicom-archive-tools sub-repo within the mri/ directory (created by the git clone command):

    cd /data/$projectname/bin/mri/
    git submodule init
    git submodule sync
    git submodule update
  3. Install MINC toolkit from http://bic-mni.github.io/

    Download the pre-compiled package for your operating system. Install required dependencies such as imagemagick. Then install your MINC toolkit package:

    run sudo dpkg i minc-toolkit<version>.deb

    Then source the MINC toolkit environment by running (for bash) source /opt/minc/minc-toolkit-config.sh or (tcsh) source /opt/minc/minc-toolkit-config.csh.

  4. Run installer to install DICOM toolkit, Perl libraries, configure environment, and setup directories:

    cd /data/$projectname/bin/mri/
    bash ./imaging_install.sh

    You will be asked for the following input:

    • What is the database name? $dbname
    • What is the database host? $dbhost
    • What is the MySQL user? $lorisuser [Use the same mysql user from the Loris installation, i.e. lorisuser]
    • What is the MySQL password?
    • What is the Linux user which the installation will be based on? $lorisadmin
    • What is the project name? $projectname
    • What is your email address?
    • What prod file name would you like to use? default: prod [leave blank]
    • Enter the list of Site names (space separated) site1 site2

    If the imaging install script reports errors in creating directories (due to /data/ mount permissions), review and manually execute mkdir/chmod/chown commands starting at imaging_install.sh:L83

    Note: The installer will allow Apache to write to the /data/ directories by adding user lorisadmin to the Apache linux group. To ensure this change takes effect, log out and log back into your terminal session before running the imaging pipeline. The installer will also set Apache group ownership of certain /data/ subdirectories.

  5. Configure paths and environment

    To help ensure Apache-writability, verify that your environment file contains the following line:

      umask 0002

    Ensure that /home/lorisadmin/.bashrc includes the statement:

    source /data/$projectname/bin/mri/environment

    Then source the .bashrc file.

  6. Set up MINC utilities for BrainBrowser visualization

    To ensure that BrainBrowser can load MINC images, the MINC toolkit must be accessible to the main LORIS codebase. (If the Loris-MRI codebase is installed on a separate machine, ensure the MINC toolkit is installed in both locations.)

    Ensure the project/config.xml file (in the main LORIS codebase) contains the following tagset, specifying the MINC toolkit path local to the main LORIS codebase (/opt/minc/ in this example):

    <!-- MINC TOOLS PATH -->
    <MINCToolsPath>/opt/minc/</MINCToolsPath>
  7. Verify filesystem permissions

As a final step, ensure that permissions on /data/$projectname and /data/incoming and their subdirectories are set such that lorisadmin and the Apache linux user can read, write and execute all contents.

The following must be recursively owned by the lorisadmin user and by Apache group:

   /data/$projectname/data/ 
   /data/$projectname/bin/mri/
   /data/incoming/
   /data/$projectname/bin/mri/dicom-archive/.prod


Installation complete. For customizations and protocol configurations, see LORIS Imaging Setup Guide.