Neuro Pipelines

Neuroimaging pipelines tailored for specific tasks and scan protocols in a multi-session, pharmacological fMRI study.

Requires Python 3.10+

Get Python 3.13 on Windows Store

Get Python 3.13 on Python.org

Available Tools

• BIDS conversion
• Event (timing) file creation and task accuracy/reaction time calculations
• Preprocessing
• First and second level analyses (GLM and gPPI) with autogenerated HTML files for reporting
• Miscellaneous utilities
• Extracting Conners 4 data
• Organizing NIH toolbox data
• Lookup brain regions for MNI coordinates

Installation

Clone the repository:

git clone https://github.com/donishadsmith/neuro_pipelines
cd neuro_pipelines

Local Workstation

Install packages directly:

pip install -r requirements.txt

Or use a virtual environment:

python -m venv venv

# Linux
source venv/bin/activate

# Windows
venv\Scripts\activate

pip install -r requirements.txt

Run Streamlit App Hub

Double click on:

• "launch_app.bat" for Windows
• "launch_app.sh" for Linux
• "launch_app.command" for MacOS

or

In terminal:

streamlit run app.py

HPC (Conda)

conda create -n venv python=3.10
source activate venv
pip install -r requirements.txt