Install and Configuration

- open terminal and type :

wget -O- http://neuro.debian.net/lists/bionic.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list

sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9

sudo apt-get update

sudo apt-get install afni

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#AFNI
export PATH=/usr/lib/afni/bin:$PATH

- to save and type :

source .bashrc

- download the release of ANTS from the official github homepage (to date, the last known version is ANTs Version 2.1.0)
- decompress the downloaded file and store it somewhere on your system, e.g. /usr/local/antsbin

- open terminal and type :

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#ANTs
export PATH=/usr/local/antsbin/ANTs.2.1.0.Debian-Ubuntu_X64:$PATH
export ANTSPATH=/usr/local/antsbin/ANTs.2.1.0.Debian-Ubuntu_X64/

- to save and type :

source .bashrc

- go to the official FSL installation page and follow the instructions.
- you can install it under /usr/local/fsl of your system
- open terminal and type :

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#FSL
FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

- to save and type :

source .bashrc

- download SPM12 from the official page
- uncompress the zip file and copy the repertory 'SPM12' and its content to the 'toolbox' folder of your Matlab, e.g. /usr/local/MATLAB/R2019a/toolbox/
- open terminal and type :

cd /usr/local/MATLAB/R2019a/toolbox/local/

sudo nano pathdef.m

- find the line %%% BEGIN ENTRIES %%% and add to the line below : matlabroot,'/toolbox/spm12:', ...

%%% BEGIN ENTRIES %%%
matlabroot,'/toolbox/spm12:', ...

- to save

- type :

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#SPM12
export SPM_PATH=/usr/local/MATLAB/R2019a/toolbox/spm12/

- to save and type :

source .bashrc

- go to the ImageJ download page, download for Linux and install it somewhere on your system, e.g. /(your_home)/Apps/
- open terminal and type :

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#ImageJ
export PATH=/home/ommaster/Apps/ImageJ:$PATH

- to save and type :

source .bashrc

- download MRIFileManager (mri_conv) from the github homepage
- unzip the downloaded file and store it somewhere on your system, e.g. /(your_home)/Apps/

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#MRIFileManager
export MRIFilePATH=/home/ommaster/Apps/Github/mri_conv/MRIFileManager/MRIManager.jar

- to save and type :

source .bashrc

- open terminal and type :

cd ~

sudo nano .bashrc

- add the following lines at the end of your .bashrc file

#MATLAB
export PATH=/usr/local/MATLAB/R2019a/bin:$PATH
export MATLABCMD=/usr/local/MATLAB/R2019a/bin/glnxa64/MATLAB

- to save and type :

source .bashrc

- open a terminal and choose or create a directory where MP3 modules will be installed

- in this directory, type :

git clone https://github.com/nifm-gin/MP3_User_Modules_Repository.git

- in your Matlab software, add this directory in the matlab path ('Set Path' menu then 'Add with subfolders')

- open a terminal and type :

sudo apt-get install git g++ python libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev 
 libfftw3-dev libtiff5-dev libpng-dev

- choose or create a directory where MRTrix will be installed.

- in this directory, type

git clone https://github.com/MRtrix3/mrtrix3.git

cd mrtrix3

./configure

./build

./set_path

- Close the terminal and start another one.

mrview

- open terminal and type :

sudo apt-get install gnupg software-properties-common wget

sudo wget -O - http://dl.bintray.com/lamyj/generic/gpg.key | sudo apt-key add -

sudo add-apt-repository "deb http://dl.bintray.com/lamyj/generic/apt $(lsb_release -cs) main"

apt-get update

sudo apt-get install dicomifier-cli