High resolution fMRI data analysis in Python, based on AFNI, FreeSurfer, ANTs, and many other tools.
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.
The latest mripy documentation is available online.
Installation (in linux/mac)
Install AFNI and FreeSurfer
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
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