Populse_mia’s third-party software installations¶

To use bricks and pipelines from mia_processes in populse_mia, it is necessary to install software as FSL, SPM, Freesurfer, ANTs…

The software access paths must be configured in Mia preferences.

Installation on Linux¶

These installation notes are based on Ubuntu 22.04.02 (and Fedora 37) which use Python3 as default (when python is typed into a command line).

/path/to/softs is the destination folder where the software will be installed, i.e.: /opt, /home/APPS or other.

If populse_mia is installed in a container using brainvisa Singulary image, it’s generally not necessary to be inside the container to install third-party software (installation on the host may be enough, but this depends on the container’s operating system and the host).
Populse_mia needs no environment variables, however to test installed third-party software outside populse_mia, the following lines must be included in the user’s .bashrc file, or, depending on the operating system, any other script file executed when a user logs on (we recommend not to use these environment variables when using populse_mia by commenting the corresponding lines in the ~/.bashrc file). It may be necessary to open a new shell or restart a session (logout / login) or execute the contents of the .bashrc file (source ~/.bashrc) for the changes to take effect:
# FSL setup
# FSL configuration is done in /home/user/.bash_profile and /home/user/Documents/MATLAB/startup.m
export PATH="$PATH:/path/to/softs/fsl_you_have_installed/bin"
export FSLOUTPUTTYPE=NIFTI
export FSLDIR=/path/to/softs/fsl_you_have_installed

# AFNI setup
## auto-inserted by @update.afni.binaries:
export PATH=$PATH:/path/to/softs/AFNI_you_have_installed/abin
## auto-inserted by @update.afni.binaries :
##    set up tab completion for AFNI programs
if [ -f $HOME/.afni/help/all_progs.COMP.bash ]
then
   source $HOME/.afni/help/all_progs.COMP.bash
fi
export R_LIBS=/path/to/softs/AFNI_you_have_installed/R

# ANTS setup
export ANTSPATH=/path/to/softs/ANTS_you_have_installed
export PATH="$ANTSPATH:$PATH"
# The following three lines should not be commented on, in order to obtain perfectly reproducible results with ANTS (as with the MRIQC pipeline, for example).
export ANTS_RANDOM_SEED=1
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export OMP_NUM_THREADS=1

# Freesurfer setup
export FREESURFER_HOME=/path/to/softs/FreeSurfer_you_have_installed
source $FREESURFER_HOME/SetUpFreeSurfer.csh>/dev/null

Installation of SPM 12 Standalone and Matlab Runtime¶

Download the desired version of standalone SPM 12.

Unzip it. For example:
cd ~/Downloads/
unzip spm12_r7771_Linux_R2019b.zip -d /path/to/soft/spmStandalone
Download and install the corresponding R20xxa/b Matlab Runtime installation for linux here.
Unzip it:
cd ~/Downloads
unzip MATLAB_Runtime_R2019b_Update_9_glnxa64.zip
And then install it (sudo is only required to install in a directory without write access):
cd MATLAB_Runtime_R2019b_Update_3_glnxa64
sudo ./install
After the installation, the following message is observed (ex. for R2019b (9.7) Matlab Runtime):
On the target computer, append the following to your LD_LIBRARY_PATH environment variable:
/usr/local/MATLAB/MATLAB_Runtime/v97/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/extern/bin/glnxa64
If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable.
Click on next in order to finish the installation.
Then if necessary (optional), create a .conf file in the /etc/ld.so.conf.d/ folder and add those previous paths in the file:
sudo nano /etc/ld.so.conf.d/your_lib.conf
# Matlab 2019b Runtime Library
/usr/local/MATLAB/MATLAB_Runtime/v97/runtime/glnxa64
/usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64
/usr/local/MATLAB/MATLAB_Runtime/v97/sys/os/glnxa64
/usr/local/MATLAB/MATLAB_Runtime/v97/extern/bin/glnxa64
Run ldconfig to update the cache (optional):
sudo ldconfig
Check this manual in case of problems during installation.
Test SPM12 Standalone and MCR installation (the second path being the path to the Matlab Runtime):
/path/to/spm_standalone/spm12/run_spm12.sh /path/to/MATLAB_Runtime/v97 eval "ver"

Installation of FSL ¶

Download fslinstaller.py (with Fedora 37, choose Linux - Centos 8) then launch the installer:
python fslinstaller.py
The installer will ask where to install FSL. Keep the default location or specify a folder:
FSL installation directory [/home/username/fsl]: /path/to/softs/fsl-6.0.6.4/
It seems that some versions of the installer automatically add the FSL configuration to ~/.bash_profile. We recommend not to use these environment variables when using populse_mia (comment out the corresponding lines in the ~/.bash_profile).
Test FSL installation on a new terminal:
/path/to/softs/fsl-6.0.6.4/bin/flirt -version

Installation of AFNI ¶

For Ubuntu, follow the quick setup of the AFNI’s team. For Fedora 37, select the Linux, Fedora chapter in the table of contents on the left.

By default, all data will be installed in $HOME. $HOME/abin can then be moved to a directory dedicated to AFNI (e.g. /data/softs/AFNI). The rest of the data installed in $HOME can be deleted if AFNI is to be used only in Mia.
Test AFNI on a new terminal:
/path/to/softs/AFNI_you_have_installed/abin/afni -ver

Installation of ANTs ¶

We strongly recommend installing ANTs via release binaries, available for macos and linux (ubuntu, centos - fedora) from ANTs v2.4.1, and Windows from v2.4.4. For this, download pre-built releases (select the desired file in the Assets section, e.g. ants-2.4.1-centos7-X64-gcc.zip) then unzip it. Some notes on this subject are available.

ANTs since v2.4.4 is also available via Conda.

The final solution for installing ANTs is to build it from source (e.g. for release < v2.4.1 for linux and macos and release < v2.4.4 for windows).
Test ANTs on a new terminal:
/path/to/softs/ANTs_you_have_installed/bin/antsRegistration --version

Installation of FreeSurfer ¶

Go to the FreeSurfer Download and Install page.

Choose the version to install (we strongly recommend installing the latest version), for example at the time of writing, version 7.x.

Select the packages or tarballs you wish to download to proceed with the installation. Some notes on this subject are available.

For Fedora 37, centos8 tar archive works fine.

Get the freesurfer License here. Copy the license received in the freesurfer folder.
Test FreeSurfer on a new terminal:
/path/to/softs/FreeSurfer_you_have_installed/bin/mris_register --version

Installation of MRtrix ¶

The following instruction resume how to build MRTrix3 from source on Linux. Further details are available on the MRtrix’s documentation

python and python-is-python3 should be installed
Install others dependencies:
sudo apt-get install git g++ libeigen3-dev zlib1g-dev libqt5opengl5-dev libqt5svg5-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev libpng-dev
Clone the MRTrix3 repository:
git clone https://github.com/MRtrix3/mrtrix3.git
Configure the MRtrix3 install (in the new mrtrix3 directory):
cd mrtrix3
./configure
Build MRtrix3:
./build

Installation on Macos¶

Installation of SPM 12 Standalone and Matlab Runtime¶

Download the spm12_r7532_BI_macOS_R2018b.zip file. Unzip it. In the same directory where run_spm12.sh can be found unzip spm12_maci64.zip.

Download the corresponding MCR for MATLAB Compiler Runtime (MCR) MCR_R2018b_maci64_installer.dmg.zip file.

Start the MATLAB Runtime installer:

double click in MCRInstaller.dmg

then right click on MCRInstaller.pkg

then choose Open with > Installer (default). The MATLAB Runtime installer starts, it displays a dialog box. Read the information and then click Next (or continue) to proceed with the installation.

Then click Install. The default MATLAB Runtime installation directory is now in /Applications/MATLAB/MATLAB_Compiler_Runtime/vXX.
Usage: Go where run_spm12.sh file can be found, then just type:
./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/vXX/
If No Java runtime is already installed, a pop-up is opened with a No Java runtime present, requesting install message.

Download Java for OS X 2017-001.

Click on Download then Open with > DiskImageMounter (default) > Ok.

Right click on the JavaForOSX.pkg then choose Open with Installer (default).

The Java for OS X 2017-001 installer starts, it displays a dialog box. Answer the questions then install.

Tested on macOS 10.13.6:

The spm12_r7771.zip file and MCR v4.13 (MATLAB R2010a) MCRInstaller.dmg file are not compatible with mia (while ./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ fmri works fine in a terminal). Using this version of spm standalone, the following message is observed in MIA: /Volumes/Users/econdami/Documents/spm/spm12Standalone/spm12Stndalone_r7771/run_spm12. sh: line 60: ./spm12.app/Contents/MacOS/spm12_maci64: No such file or directory.

Installation of others software¶

Please follow the instruction in the documentation of each third-party software.

Installation on Windows¶

Please follow the instruction in the documentation of each third-party software.

Populse_mia’s third-party software installations¶

Installation on Linux¶

Installation of SPM 12 Standalone and Matlab Runtime¶

Installation of FSL¶

Installation of AFNI¶

Installation of ANTs¶

Installation of FreeSurfer¶

Installation of MRtrix¶

Installation on Macos¶

Installation of SPM 12 Standalone and Matlab Runtime¶

Installation of others software¶

Installation on Windows¶

Installation of FSL ¶

Installation of AFNI ¶

Installation of ANTs ¶

Installation of FreeSurfer ¶

Installation of MRtrix ¶