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easy fMRI project (V1.8B4200 beta)

Introduction

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/.

Dependencies

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

How to install easy fMRI

Pre-install for Windows 10 users:

-- 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

STEP A) Copy Files

-- 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)

STEP B) Install FSL 5.0.10 or above

-- 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)

STEP D) Install AFNI 17.3.06 or above

-- 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

STEP D) Install Python 3.6.x

-- 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

STEP E) Run easy fMRI

After restarting your computer, open a terminal and run easyfmri:

ezfmri

How to upgrade easy fMRI

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

An example of environment variables

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

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