This Readme covers release 20.0 of the LORIS Imaging Insertion Pipeline for Ubuntu or CentOS systems
This repo accompanies the LORIS neuroimaging data platform main repo, release 20.0.*.
For documentation and detailed setup information, please see the LORIS-MRI documentation for your installed version.
This repo can be installed on 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.
- MINC toolkit (step 2 below)
- DICOM toolkit (step 3 below)
On Ubuntu, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will apt-get install dcmtk.
The following installation should be run by the $lorisadmin user. sudo permission is required. See aces/Loris README.md for further information.
1. Create directories and download Loris-MRI code
sudo mkdir -p /data/$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
Download the pre-compiled package for your operating system. Install required dependencies such as imagemagick. Then install your MINC toolkit package:
sudo dpkg -i minc-toolkit<version>.deb
Then source the MINC toolkit environment by running (for bash)
source $mincToolsDirectory/minc-toolkit-config.sh or (tcsh)
$mincToolsDirectory is the path where the MINC toolkit is installed (e.g.
/opt/minc/$mincToolsVersion/ for more recent installs)
3. Run installer to set up directories, configure environment, install Perl libraries and DICOM toolkit:
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:L97
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.
4. Configure paths and environment
Ensure that /home/lorisadmin/.bashrc includes the statement:
Then source the .bashrc file.