findviz 0.1.4

FIND Viewer: FMRI Interactive Navigation and Discovery Viewer

FINDVIZ: FMRI Interactive Navigation and Discovery Viewer

Background

FINDVIZ is a browser-based visualization tool for visual exploration of fMRI data with a focus on pattern discovery. It supports the visualization of NIFTI, GIFTI, and CIFTI file formats, and time series data. Visualizations are produced using PlotlyJS.

Installation

Using pip

pip install findviz

Quick Start

To launch the application and upload an fMRI dataset through the web interface, run the following command in your terminal:

findviz

This will launch the application in your default browser. FINDVIZ was tested on Google Chrome (v134). We recommend using Chrome for the best experience.

Command Line Interface

FINDVIZ also supports uploading fMRI data from the command line:

# Launch with NIFTI files
findviz --nifti-func func.nii.gz --nifti-anat anat.nii.gz

# Launch with GIFTI files
findviz --gifti-left-func left.func.gii --gifti-right-func right.func.gii --gifti-left-mesh left.surf.gii --gifti-right-mesh right.surf.gii

# Launch with CIFTI files
findviz --cifti-dtseries data.dtseries.nii --cifti-left-mesh left.surf.gii --cifti-right-mesh right.surf.gii

# Add time series data
findviz --nifti-func func.nii.gz --timeseries timeseries1.csv timeseries2.csv

Features

• Multi-format Support: Visualize NIFTI, GIFTI, and CIFTI neuroimaging data
• Interactive Visualization: Explore nifti data with orthogonal and montage views, and GIFTI and CIFTI data with 3D surface views
• Time Series Visualization: Visualize synchronized physiological, experimental design, and other time series data.
• Preprocessing Tools: Apply normalization, filtering, detrending, and smoothing
• Analysis Tools: Analysis functions for facilitating fMRI exploration and discovery
• Customizable Display: Adjust colormaps, thresholds, and visualization parameters
• State Management: Save and load visualization states

Data Formats

FINDVIZ supports the following neuroimaging data formats:

• NIFTI (.nii, .nii.gz): 3D and 4D functional and anatomical brain images
• GIFTI (.gii): Surface-based brain data for left and right hemispheres
• CIFTI (.dtseries.nii): Combined surface and volume data
• Time Series (.csv, .txt): Custom time course data for visualization alongside fMRI data
• Task Design (.csv, .tsv): Experimental design matrices for visualization alongside fMRI data

Documentation

Coming soon!

Limitations

• FINDVIZ displays fMRI data in voxel coordinates, and does not support the overlay of images with different spatial resolutions, even in the same coordinate space (e.g. MNI152). Thus, anatomical and/or functional images should be resampled to the same resolution before uploading.

• FINDVIZ is not a preprocessing tool. Preprocessing options are limited to options that faciliate visualization, including normalization, detrending, smoothing, and temporal filtering. For end-to-end preprocessing, we recommend using more comprehensive tools such as FMRIPREP.

Requirements

• Python 3.10+
• Flask 3.0.3+
• Matplotlib 3.9.2+
• Nilearn 0.10.4+
• Plotly 5.23.0+

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use FINDVIZ in your research, please cite:

Bolt, T. (2025). FINDVIZ: FMRI Interactive Navigation and Discovery Viewer. 
https://github.com/tsb46/fmri-findviz