Install TFCE_mediation

Dependencies

TFCE_mediation should work with any UNIX based system. It has been tested on Ubuntu 14.04 and 16.04, Arch Linux, and OSX

Required

• If TkInter is not already installed: python-tk
• For Ubuntu 16.04 the python-dev package will need to be installed

For debian based systems: sudo apt-get install python-dev python-tk

Recommended

• FSL
• Neurodebian repository
• PIP

Recommended for parallelization:

• GNU Parallel

or

• For personal installation of HTCondor (i.e., Condor), you can follow the instructions here

Installation

Option 1 (System-wide PIP installation)

PIP Install (recommended) The python dependencies will automatically be installed.

sudo -H pip install -U git+https://github.com/trislett/TFCE_mediation.git

Option 2 (using a virtual environment)

virtualenv python2env
source python2env/bin/activate
pip install -U tfce-mediation

Maybe add the sourced environment to your bashrc (echo source $PWD/python2env/bin/activate >> ~/.bashrc)

Option 3 (install from source)

requires the following python packages: numpy, scipy, matplotlib, nibabel, cython, scikit-learn, joblib):

git clone https://github.com/trislett/TFCE_mediation.git
cd TFCE_mediation
sudo python setup.py install

Note: for OSX you may need to turn off SIP or use geodesic FWHM smoothing in step0-vertex instead of Freesurfer's surface smoothing.

Optional components for TFCE_mediation

TMI_Viewer: Vertex/Voxel Rendering for TMI files

Quick install:

1. Dependencies

• Ubuntu 14.04

sudo apt-get install tcl-vtk
sudo apt-get install vtk6 python-vtk python-qt4

• Ubuntu 16.04

sudo apt-get install vtk6 python-vtk python-qt4

• OSX

brew install vtk

2. Install using PIP

sudo -H pip install -U tmi_viewer

TM_ADDONS: Support files for Geodesic FWHM smoothing, Blender Scenes for PLY images, and more.

Quick install:

git clone https://github.com/trislett/tm_addons.git
cd tm_addons
echo export TM_ADDONS=$PWD >> ~/.bashrc # optional
bash download_9mm_geodesic_fwhm_files.sh # download geodesic FWHM support files