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High resolution fMRI data analysis in Python, based on AFNI, FreeSurfer, ANTs, and many other tools.

Project description

Introduction

This is a collection of handy small tools for analyzing neuroimaging data (esp. high resolution fMRI), which can be used both as a Python package and a set of command line tools. It is a useful augmentation to the AFNI tool chain.

Installation (in linux/mac)

Install AFNI and FreeSurfer

Please follow the instructions in their official websites (AFNI, FreeSurfer).

Install mripy

Download and install the mripy package:

$ pip install mripy

Set $PATH for using the package scripts in the terminal. For bash, the commands look like:

$ vi ~/.bashrc
$ export PATH="path/to/mripy/scripts":$PATH

The path could be something like “~/anaconda3/lib/Python3.8/site-packages/mripy/scripts”.

Download and install the dependencies:

$ pip install nibabel deepdish

Install neuropythy docker (for HCP retinotopy altas)

First install docker for your OS, then pull the neuropythy image:

# Pull a particular version
$ docker pull nben/neuropythy@sha256:2541ee29a8d6bc676d9c3622ef4a38a258dd90e06c02534996a1c8354f9ac888

# Give it a tag
$ docker tag b38ebfcf6477 nben/neuropythy:mripy

More information about the HCP retinotopy altas and the neuropythy package can be found in Noah C. Benson’s website.

Project details


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