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Installation

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Francois edited this page Nov 26, 2020 · 10 revisions

Requirements

IntrAnat requires the installation of:

  • BrainVISA: Version > 4.6.1
  • Matlab: Requires a Matlab license to run SPM12 for MNI normalization
  • SPM12: For MNI normalization and volume co-registration
  • ANTs 2.2: For volume co-registration (optional)
  • FreeSurfer 6.0: For importing the result of the FreeSurfer T1 MRI segmentation pipeline (optional)

Supported operating systems:

  • Ubuntu 16.04: Reference for all the instructions below
  • CentOS 7:
    • For CentOS/Fedora/RHEL, similar packages are available for install using "sudo yum install" instead of "sudo apt install", but their name might have to be updated.
  • Other Linux distributions: Might work but haven't been tested yet, the main limiting factor for portability being BrainVISA
  • Windows 10/WSL: Linux subsystem on Windows 10 / Ubuntu 16.04
    • Almost everything works just as with a Ubuntu 16.04,
    • WSL can run only the latest versions of Matlab (>= 2018b), but Matlab can be installed on the Windows system and called from WSL/IntrAnat

Install Ubuntu packages

Instructions for Unbuntu 16.04.

Update your system:

sudo apt update
sudo apt dist-upgrade

FreeSurfer dependencies:

sudo apt install build-essential libjpeg62 libxss1 libgomp1 tcsh bc

ANTS dependencies:

sudo apt install cmake-curses-gui gcc g++ zlib1g-dev

BrainVISA/IntrAnat:

sudo apt install libtinfo-dev libapt-pkg-dev git libav-tools mencoder libglm-dev 
wget http://ftp.br.debian.org/debian/pool/main/a/apt/libapt-pkg4.12_1.0.9.8.4_amd64.deb
dpkg -i libapt-pkg4.12_1.0.9.8.4_amd64.deb
rm libapt-pkg4.12_1.0.9.8.4_amd64.deb

Install IntrAnat

Define installation directory:

mkdir $HOME/IntrAnat
export INTRANAT_INSTALL=$HOME/IntrAnat

Clone the GitHub repository:

cd $INTRANAT_INSTALL
git clone https://github.com/ftadel/IntrAnat

Checkout brainvisa_4.6 branch in the git repository:

cd $INTRANAT_INSTALL/IntrAnat/
git checkout --track origin/brainvisa_4.6

Download BrainVISA

The current official version of BrainVISA (4.6.1) contains bugs in Anatomist that make IntrAnat interface unusable. We distribute temporarily a patched version of BrainVISA 4.6.2 on an alternate website, until the BrainVISA developers release a new version including these bug fixes.

A last option is to compile BrainVISA with bv_maker on your system.

Install BrainVISA

Start the installer:

chmod u+x brainvisa-4.6-install
./brainvisa-4.6-install
  • Set the installation to: /home/USERNAME/IntrAnat/brainvisa-4.6.1.
  • Use the default options

Set up epilepsy toolbox:

ln -s $INTRANAT_INSTALL/IntrAnat/epilepsy-toolbox $INTRANAT_INSTALL/brainvisa-4.6.1/brainvisa/toolboxes/epilepsy

Add the electrode models:

ln -s $INTRANAT_INSTALL/IntrAnat/electrode_models $INTRANAT_INSTALL/brainvisa-4.6.1/share/brainvisa-share-4.6/electrode_models

Start Brainvisa, set up and update the databases:

mkdir $INTRANAT_INSTALL/brainvisa_db
$INTRANAT_INSTALL/brainvisa-4.6.1/BrainVISA

In the BrainVISA interface:

  • In the window "Update databases", click on the button "Update", then close the figure
  • If you get the window "Welcome to BrainVISA" click on button "Open preferences", otherwise select menu "BrainVISA > Preferences"
    • In the "Databases" section, click on "Add", then select folder $INTRANAT_INSTALL/brainvisa_db, then click "OK"
    • Close BrainVISA
  • Add your freesurfer database: Read the help in BrainVISA's FreeSurfer toolbox

Install additional packages in BrainVISA's Python environment if necessary:

  • openpyxl:
cd $INTRANAT_INSTALL/
source $INTRANAT_INSTALL/brainvisa-4.6.1/bin/bv_env.sh $INTRANAT_INSTALL/brainvisa-4.6.1
wget https://files.pythonhosted.org/packages/d9/dd/5952829956827de7ff36eb70877fdffd6dbfacb670fae05eb7ccba52ace7/openpyxl-2.5.5.tar.gz
tar zxvf openpyxl-2.5.5.tar.gz
rm openpyxl-2.5.5.tar.gz
cd openpyxl-2.5.5/
python setup.py install
  • jdcal
  • et_xmlfile

Specific instructions for Windows 10/WSL:

  • Delete brainvisa/lib/libxcb* to avoid the errors "libxcb-dri3.so.0: undefined symbol: xcb_send_fd"
  • Delete additional duplicated libraries
  • cd $INTRANAT_INSTALL/brainvisa-4.6.1/lib
  • rm libxcb* libgcc_s* libpcre* libstdc++* libtinfo* libdl* libz*

Specific instructions for Mandriva2008:

  • rm libgcc_s* libstdc++* libdl* libz*
  • Install in brainvisa Python environment: jdcal, et_xmlfile, openpyxl

Install FreeSurfer

Download FreeSurfer 6.0:

cd $INTRANAT_INSTALL
wget -O freesurfer.tgz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
tar zxvf freesurfer.tgz

Add the FreeSurfer configuration to your .bashrc:

grep -q -F "FREESURFER_HOME=" ~/.bashrc || printf "\n# FREESURFER\nexport FREESURFER_HOME=$INTRANAT_INSTALL/freesurfer\nsource \$FREESURFER_HOME/SetUpFreeSurfer.sh\n" >> ~/.bashrc
rm freesurfer.tgz

Get a license file for FreeSurfer (http://surfer.nmr.mgh.harvard.edu/registration.html) and save it in $INTRANAT_INSTALL/freesurfer/license.txt Example:

printf "[email protected]\n34309\n *COj3JXOXnbes\n FSCI/SECcEOfM" > $INTRANAT_INSTALL/freesurfer/license.txt

Install ANTs

Get and compile ANTs >= 2.2.0:

cd $INTRANAT_INSTALL
wget -O ANTs.tgz https://github.com/stnava/ANTs/tarball/master
tar zxvf ANTs.tgz
rm ANTs.tgz
mv ANTsX-ANTs* ANTs
cd ANTs
mkdir build
cd build
ccmake ../

make

Add the ANTs configuration to your .bashrc:

grep -q -F "ANTSPATH=" ~/.bashrc || printf "\n# ANTs\nexport ANTSPATH=$INTRANAT_INSTALL/ANTs/build/bin/\nexport PATH=$INTRANAT_INSTALL/ANTs/Scripts:\$ANTSPATH:\$PATH\nexport ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4\n" >> ~/.bashrc

Install MATLAB

Install any version of Matlab. Make sure it is in the system PATH.

Install SPM12:

cd $INTRANAT_INSTALL
wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip
unzip spm12.zip
rm spm12.zip

Set the program paths in BrainVISA:

  • Start BrainVISA: $INTRANAT_INSTALL/brainvisa-4.6.1/BrainVISA
  • Open menu BrainVISA > Preferences: Set SPM path to $INTRANAT_INSTALL/spm12
  • Close BrainVISA

Matlab on Windows 10/WSL

You can either install MATLAB in WSL/Ubuntu, or install the Windows version and create a link to matlab.exe inside the Ubuntu PATH. For example:

sudo -s
printf '#!/bin/bash\n/mnt/c/Program\ Files/MATLAB/R2017b/bin/matlab.exe -nodesktop -wait "$@"\nexit $?' > /usr/local/bin/matlab 
chmod a+x /usr/local/bin/matlab

Exchanging data between the Ubuntu and Windows drives:

Start IntrAnat

Create startup scripts:

cd $INTRANAT_INSTALL
printf "#!/bin/bash\nsource $INTRANAT_INSTALL/brainvisa-4.6.1/bin/bv_env.sh $INTRANAT_INSTALL/brainvisa-4.6.1\ncd IntrAnat\npython ImageImport.py" > ImageImport.sh
printf "#!/bin/bash\nsource $INTRANAT_INSTALL/brainvisa-4.6.1/bin/bv_env.sh $INTRANAT_INSTALL/brainvisa-4.6.1\ncd IntrAnat\npython locateElectrodes.py" > locateElectrodes.sh
printf "#!/bin/bash\nsource $INTRANAT_INSTALL/brainvisa-4.6.1/bin/bv_env.sh $INTRANAT_INSTALL/brainvisa-4.6.1\ncd IntrAnat\npython groupDisplay.py" > groupDisplay.sh
chmod a+x *.sh

Manual execution:

cd ~/IntrAnat
source brainvisa-4.6.1/bin/bv_env.sh
cd IntrAnat
python ImageImport.py

Or all in one line:

cd ~/IntrAnat && source brainvisa-4.6.1/bin/bv_env.sh && cd IntrAnat && python ImageImport.py

Set program paths:

  • Open ImageImport, go to the tab "Preferences"
  • Set path to SPM12: $INTRANAT_INSTALL/spm12
  • Set path to ANTs: $INTRANAT_INSTALL/ANTs-build
  • Set path to FreeSurfer: $INTRANAT_INSTALL/freesurfer (should be set automatically if the FreeSurfer path is properly set in the BrainVISApreferences )
  • Click on button "Save preferences"

Update IntrAnat from GitHub:

cd ~/IntrAnat/IntrAnat
git pull

Install MRIConvert

MRIConvert is not needed for running IntrAnat, but is a very useful tool for converting DICOM images into .nii files. https://lcni.uoregon.edu/downloads/mriconvert

cd $INTRANAT_INSTALL
wget -O MRIConvert.tgz https://lcni.uoregon.edu/downloads/mriconvert/MRIConvert-2.1.0-x86_64-rhel.tar.gz/at_download/file
tar zxvf MRIConvert.tgz
rm MRIConvert.tgz
cd MRIConvert-*
chmod a+x install.sh
sudo ./install.sh

Lausanne2008 parcellation

These scripts are not publicly available yet...

Install FSL:

sudo apt-get install neurodebian
sudo apt-get update
sudo apt-get install fsl-complete 
sudo pip install nypipe
sudo pip install nibabel
sudo pip install networkx==1.11

Edit .bashrc, add at the end:

source /usr/share/fsl/5.0/etc/fslconf/fsl.sh
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