Easy fMRI is an open source toolbox for the Human Brain Mapping and Decoding. This project is developing by Muhammad Yousefnezhad, iBRAIN Group, Nanjing University of Aeronautics and Astronautics, China.
The project website is https://easyfmri.github.io/ or https://easyfmri.sourceforge.io/.
Easy fMRI needs following software:
-Platform: Linux (recommended), Mac, Windows (via Linux Virtual Machine, or Bash for Windows 10 or above)
-Python3 (version=3.6.2 or above)
-FSL (version=5.0.10 or above) for preprocessing steps
-AFNI & SUMA (version=17.3.06 or above) for 3D visualization
-CUDA for GPU-based algorithms
-CUDNN for GPU-based algorithms
-Tensorflow for Gradient-based Optimization and Learning
-- Install Windows Subsystem for Linux https://docs.microsoft.com/en-us/windows/wsl/install-win10
NOTE: You have to install UBUNTU Linux from Windows Store.
-- Install Xming X Server for Windows: https://sourceforge.net/projects/xming/files/latest/download
-- Open command prompt (press Windows key + R, then in run window type cmd and press enter)
-- Open bash via cmd:
bash
-- Set Display:
echo "export DISPLAY=:0.0" >> ~/.profile
source ~/.profile
Now you can install easy fMRI same as a linux system
-- Download easy fMRI files:
From GitHub:
git clone https://github.com/easyfmri/easyfmri.git ~/.easyfmri
From SourceForge Git:
git clone git://git.code.sf.net/p/easyfmri/code ~/.easyfmri
From SourceForge as a zip file
unzip easyfMRI.<version>.zip
mv easyfmri .easyfmri
-- Copy ezfmri to /usr/bin/local
cd ~/.easyfmri/Script
./cp_script
-- Set environment variables (see example at the end)
-- Register on FSL website
-- Download fslinstaller.py
-- Run following for downloading installation file (e.g. In version 5.0.10, the file name is fsl-5.0.10-macOS_64.tar.gz for Mac or fsl-5.0.10-centos7_64.tar.gz for all Linux distribution)
For Linux:
python2 fslinstaller.py -o
md5sum fsl-5.0.10-centos7_64.tar.gz
For Mac:
python2 fslinstaller.py -o
md5sum fsl-5.0.10-macOS_64.tar.gz
-- Install the downloaded file:
For Linux:
python2 fslinstaller.py -f fsl-5.0.10-centos7_64.tar.gz -M
For Mac:
python2 fslinstaller.py -f fsl-5.0.10-macOS_64.tar.gz -M
-- Set environment variables (see example at the end)
-- Download AFNI
-- Extract AFNI to ~/abin
-- Set environment variables (see example at the end)
NOTE: For Ubuntu-based Linux, you have to install following packages:
sudo apt-get install -y tcsh xfonts-base python-qt4 gsl-bin netpbm gnome-tweak-tool libjpeg62 xvfb xterm vim curl
sudo apt-get install -y libglu1-mesa-dev libglw1-mesa libxm4 build-essential
-- Download Anaconda3 and Install Python3 by using Anaconda3
For Linux:
sh Anaconda3-<version>-Linux<platform>.sh
For Mac: click PKG file and continue installation.
-- Set environment variables (see example at the end)
-- Install all packages in ~/.easyfmri/PyPackage directory
cd ~/.easyfmri/PyPackage
pip install *
-- Install MPI packages:
conda install mpi4py
-- Install Tensorflow package:
For CPU version:
pip install tensorflow
For GPU Vesion: You must install CUDA and CuDNN. Then, you can install Tensorflow
Note: By employing CUDA 9.0, CUDNN 7.0 and Ubuntu 16.04.x, you can use following command to install tensorflow:
pip install tensorflow-gpu
After restarting your computer, open a terminal and run easyfmri:
ezfmri
For updating a new version, just replace the old files with the new files.
Note: default directory for easy fMRI is a hidden folder in ~/.easyfmri
rm -R ~/.easyfmri
git clone https://github.com/easyfmri/easyfmri.git ~/.easyfmri
You can install this script automatically as follows:
For Linux:
cd ~/.easyfmri/Script
./install_script_linux
For Mac:
cd ~/.easyfmri/Script
./install_script_mac
Or just copy following to in .profile or .bashrc and restart your computer
######################################
# Enable ("1") or Disable ("0") features #
######################################
export EN_EZFMRI="1"
export EN_PYTHON="1"
export EN_PYTHON_ALIAS="1"
export EN_AFNI="1"
export EN_FSL="1"
export EN_CUDA="1"
export EN_BASH="1"
export EN_MC="1"
export EN_COLOR="1"
######################################
# Directories #
######################################
export INSTALL_DIR="$HOME" # Base dir for Anaconda, easy fMRI, and AFNI
export FSLDIR="/usr/local/fsl" # for FSL 5.0.10
export ANACON_PATH="$INSTALL_DIR/anaconda3/bin"
export AFNI_PATH="$INSTALL_DIR/abin"
export CUDA_HOME="/usr/local/cuda"
# export FSLDIR="/usr/share/fsl/5.0" # for FSL 5.0.9
# export DISPLAY=:0.0 # Enable for Windows 10
######################################
# Scripts #
######################################
######## Easy fMRI
if (( $EN_EZFMRI != "0" )); then
export EASYFMRI="$INSTALL_DIR/.easyfmri"
fi
######## Python
if (( $EN_PYTHON != "0" )); then
export PATH="$ANACON_PATH:$PATH"
fi
if (( $EN_PYTHON_ALIAS != "0" )); then
alias python="python -m IPython"
alias python3="python -m IPython"
fi
######## AFNI
if (( $EN_AFNI != "0" )); then
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
export DYLD_FALLBACK_LIBRARY_PATH="$HOME/abin"
export PATH="/usr/local/bin:$AFNI_PATH:$PATH"
fi
####### FSL
if (( $EN_FSL != "0" )); then
. $FSLDIR/etc/fslconf/fsl.sh
export PATH="$FSLDIR/bin:$PATH"
fi
####### CUDA
if (( $EN_CUDA != "0" )); then
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$CUDA_HOME/lib"
export LD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$CUDA_HOME/lib:/usr/local/cuda/lib64/"
export PATH="$CUDA_HOME/bin:$PATH"
fi
####### BASH
if (( $EN_BASH != "0" )); then
[ -f /usr/local/etc/bash_completion ] && . /usr/local/etc/bash_completion
fi
####### MC
if (( $EN_MC != "0" )); then
alias mc=". /usr/local/opt/midnight-commander/libexec/mc/mc-wrapper.sh"
fi
####### BASH COLOR
if (( $EN_COLOR != "0" )); then
# Define Colors
C_DEFAULT="\[\033[m\]"
C_WHITE="\[\033[1m\]"
C_BLACK="\[\033[30m\]"
C_RED="\[\033[31m\]"
C_GREEN="\[\033[32m\]"
C_YELLOW="\[\033[33m\]"
C_BLUE="\[\033[34m\]"
C_PURPLE="\[\033[35m\]"
C_CYAN="\[\033[36m\]"
C_LIGHTGRAY="\[\033[37m\]"
C_DARKGRAY="\[\033[1;30m\]"
C_LIGHTRED="\[\033[1;31m\]"
C_LIGHTGREEN="\[\033[1;32m\]"
C_LIGHTYELLOW="\[\033[1;33m\]"
C_LIGHTBLUE="\[\033[1;34m\]"
C_LIGHTPURPLE="\[\033[1;35m\]"
C_LIGHTCYAN="\[\033[1;36m\]"
C_BG_BLACK="\[\033[40m\]"
C_BG_RED="\[\033[41m\]"
C_BG_GREEN="\[\033[42m\]"
C_BG_YELLOW="\[\033[43m\]"
C_BG_BLUE="\[\033[44m\]"
C_BG_PURPLE="\[\033[45m\]"
C_BG_CYAN="\[\033[46m\]"
C_BG_LIGHTGRAY="\[\033[47m\]"
# Set Terminal Colors
export CLICOLOR=1
export LSCOLORS=GxacCxDxBxegedabagaced
alias ls='ls -GFh'
export PS1="\n$C_LIGHTPURPLE\u$C_DEFAULT@$C_LIGHTCYAN\h$C_DEFAULT:$C_LIGHTBLUE\W$C_DEFAULT\$$C_LIGHTYELLOW "
if (( $EUID != 0 )); then
export LSCOLORS=GxacCxDxBxegedabagaced
export PS1="\n$C_LIGHTGREEN\u$C_DEFAULT@$C_LIGHTCYAN\h$C_DEFAULT:$C_LIGHTBLUE\W$C_DEFAULT\$$C_LIGHTYELLOW "
fi
fi