diff --git a/README.md b/README.md
index 84a1256f4..22b54c7be 100644
--- a/README.md
+++ b/README.md
@@ -6,11 +6,12 @@ For documentation and detailed setup information, please see the [LORIS-MRI docu
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.
# System Requirements
- * Perl
- * Python 3 with pip3 and virtualenv (step 2 below)
- * MINC toolkit (step 3 below)
- * DICOM toolkit (step 4 below)
- * tpcclib (for HRRT PET only) (step 5 below)
+
+* Perl
+* Python 3 with pip3 and virtualenv (step 2 below)
+* MINC toolkit (step 3 below)
+* DICOM toolkit (step 4 below)
+* tpcclib (for HRRT PET only) (step 5 below)
On Ubuntu, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will _apt-get install dcmtk_.
@@ -19,17 +20,39 @@ For CentOS: The [LORIS wiki](https://github.com/aces/Loris/wiki/Imaging-D
The following installation should be run by the `$lorisadmin` user. `sudo` permission is required.
See [aces/Loris](https://github.com/aces/loris) README.md for further information.
+# Dependencies
+
+## General
+
+```bash
+# ubuntu build essential packages useful for building
+sudo apt install build-essential checkinstall cmake
+```
+
+## Perl CPAN
+
+Update Perl dependency with:
+
+```bash
+sudo perl -MCPAN -e shell
+
+# then enter these two commands
+
+cpan[1]> install CPAN
+cpan[2]> reload cpan
+```
+
# Installation
#### 1. Create directories and download Loris-MRI code
- ```bash
- sudo mkdir -p /data/$projectname
- sudo mkdir -p /opt/$projectname/bin/mri
- sudo chown -R lorisadmin:lorisadmin /data/$projectname
- sudo chown -R lorisadmin:lorisadmin /opt/$projectname
- cd /opt/$projectname/bin
- ```
+```bash
+sudo mkdir -p /data/$projectname
+sudo mkdir -p /opt/$projectname/bin/mri
+sudo chown -R lorisadmin:lorisadmin /data/$projectname
+sudo chown -R lorisadmin:lorisadmin /opt/$projectname
+cd /opt/$projectname/bin
+```
Get the code: Download the latest release from the
[releases page](https://github.com/aces/Loris-MRI/releases)
@@ -47,65 +70,90 @@ sudo apt install virtualenv
#### 3. Install MINC toolkit from http://bic-mni.github.io/
-Download the pre-compiled package for your operating system. Install required dependencies such as _imagemagick_. Then install your MINC toolkit package:
+- Install MINC dependencies:
+
+```bash
+# deps
+sudo apt-get install libc6 libstdc++6 imagemagick perl
+
+# Install required dependencies such as _imagemagick_.
+sudo apt-get install libgl1-mesa-glx libglu1-mesa
+```
+
+- Download the MINC pre-compiled package for your operating system from http://bic-mni.github.io/.
+
+- Then install the MINC toolkit package:
+
+```bash
+# main minc lib
+sudo dpkg -i minc-toolkit-.deb
+```
+
+- Check the model is installed in `/opt/minc/share`
- ```bash
- sudo dpkg -i minc-toolkit.deb
- ```
+- Then source the MINC toolkit environment, where `$mincToolsDirectory` is the path where the MINC toolkit is installed (e.g. `/opt/minc/` OR `/opt/minc/$mincToolsVersion/` for more recent installs)
- Then source the MINC toolkit environment by running (for bash)
- `source $mincToolsDirectory/minc-toolkit-config.sh` or (tcsh)
- `source $mincToolsDirectory/minc-toolkit-config.csh`,
+```bash
+# bash
+source $mincToolsDirectory/minc-toolkit-config.sh
- where `$mincToolsDirectory` is the path where the MINC toolkit is installed (e.g. `/opt/minc/` OR `/opt/minc/$mincToolsVersion/` for more recent installs)
+# tcsh
+source $mincToolsDirectory/minc-toolkit-config.csh
+```
-For the defacing scripts, you will also need to download the pre-compiled `bic-mni-models` and `beast` data and model packages for you operation system.
+- For the defacing scripts, you will also need to download the pre-compiled `bic-mni-models` and `beast` data and model packages for you operation system.
- ```bash
- sudo dpkg -i bic-mni-models-.deb
- sudo dpkg -i beast-library-.deb
- ```
+```bash
+sudo dpkg -i bic-mni-models-.deb
+sudo dpkg -i beast-library-.deb
+
+# also check they are installed in `/opt/minc/share`
+```
#### 4. Run installer to set up directories, configure environment, install Perl libraries and DICOM toolkit:
- ```bash
- cd /opt/$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? $projectname
- * What is your email address?
- * What prod file name would you like to use? default: prod [leave blank]
-
- If the imaging install script reports errors in creating directories
- (due to `/data/` mount permissions), review and manually execute
- `mkdir/chmod/chown` commands starting at
- [imaging_install.sh:L97](https://github.com/aces/Loris-MRI/blob/main/imaging_install.sh#L97)
-
- Note: The installer will allow Apache to write to the `/data/` and `/opt/` directories by
- adding user `lorisadmin` to the Apache linux group. To ensure this change takes
- effect, log out and log back into your terminal session before running the
- imaging pipeline. The installer will also set Apache group ownership of certain
- `/data/` and `/opt/` subdirectories.
+```bash
+cd /opt/$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? $projectname
+* What is your email address?
+* What prod file name would you like to use? default: prod [leave blank]
+
+If the imaging install script reports errors in creating directories
+(due to `/data/` mount permissions), review and manually execute
+`mkdir/chmod/chown` commands starting at
+[imaging_install.sh:L97](https://github.com/aces/Loris-MRI/blob/main/imaging_install.sh#L97)
+
+Note: The installer will allow Apache to write to the `/data/` and `/opt/` directories by
+adding user `lorisadmin` to the Apache linux group. To ensure this change takes
+effect, log out and log back into your terminal session before running the
+imaging pipeline. The installer will also set Apache group ownership of certain
+`/data/` and `/opt/` subdirectories.
#### 5. HRRT PET
For HRRT PET, install [tpcclib](http://www.turkupetcentre.net/tpcclib-doc/md_install.html).
+Follow the [install instructions](http://www.turkupetcentre.net/petanalysis/sw_install.html).
#### 6. Configure paths and environment
- Ensure that `/home/lorisadmin/.bashrc` includes the statement:
+Ensure that `/home/lorisadmin/.bashrc` includes the statement:
+
+```bash
+source /opt/$projectname/bin/mri/environment
+```
- ```source /opt/$projectname/bin/mri/environment```
+Then source the `.bashrc` file.
- Then source the `.bashrc` file.
**INSTALLATION COMPLETE!**