simnibs-reader

Documentation for version 0.4.0

See the changelog.

Load, extract, clean and analyze SimNIBS e-field NIfTI outputs — in one line.

simnibs-reader is a lightweight Python library that turns SimNIBS simulation results into analysis-ready ROI data with built-in outlier removal, smoothing, statistics and export.

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Installation

pip install simnibs-reader

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Quick Example

import simnibs_reader as snr

sim = snr.simulation("/path/to/simnibs/simulation")

# Extract ROI, clean, get stats — 3 lines
roi = sim.magnE.get_roi(mask="my_roi.nii.gz")
cleaned = roi.postprocess(smooth_fwhm=2.0, outlier_method="iqr")
cleaned.stats()
# {'mean': 0.142, 'median': 0.138, 'std': 0.031, 'max': 0.241, ...}

Targets given in MNI coordinates work on native-space volumes too — attach the segmentation and the deformation field does the rest:

sim.set_segmentation(snr.segmentation("/path/to/m2m_0001"))
roi = sim.magnE_native.get_roi(coords=[28, -8, 54], coords_space="mni")

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Ecosystem

• SimNIBS

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  The core simulation platform for non-invasive brain stimulation.

  Documentation

• simnibs-modular

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  Modular pipeline components for SimNIBS workflows.

  GitHub Pages · Repo

• simnibs-analyze

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  Statistical analysis tools for SimNIBS outputs.

  GitHub Pages · Repo

• OptiStims

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  End-to-end automated stroke lesion-aware tDCS pipeline.

  GitHub Pages · Repo