shimadzu_fnirs_converter

Shimadzu fNIRS TXT → SNIRF (.snirf) & MNE FIF (.fif)

Convert Shimadzu proprietary TXT exports into open neuroimaging formats for modern, reproducible pipelines.

Shimadzu raw files are not directly compatible with most analysis toolkits.
This package converts them into SNIRF (standard) and MNE FIF (native) formats for seamless use in Python/MATLAB ecosystems.

Compatible with:

• MNE-Python
• Homer3
• NIRS-KIT
• Brainstorm
• any SNIRF workflow

---

Features

• TXT → SNIRF
• TXT → MNE FIF (native Raw object)
• Optode/channel geometry parsing
• Origin / others coordinate support
• Event & trigger integration
• Python API + CLI
• Batch processing
• NumPy 2 compatible
• pytest tested
• Zenodo DOI archived releases

---

Installation

From PyPI (recommended)

pip install shimadzu_fnirs_converter

### Development install
```bash
git clone https://github.com/Aria031/shimadzu_fnirs_converter
cd shimadzu_fnirs_converter
pip install -e .

Quick Start

Python API

Save both FIF + SNIRF

from shimadzu_fnirs_converter import convert

convert(
    txt_path="raw_data.TXT",
    origin_path="origin.csv",
    others_path="others.csv",
    out_fif="sub01_raw.fif",
    out_snirf="sub01_raw.snirf",
    subject="sub-01",
)

Save only FIF (MNE)

from shimadzu_fnirs_converter import convert_fif

convert_fif(
    txt_path="raw_data.TXT",
    origin_path="origin.csv",
    others_path="others.csv",
    out_fif="sub01_raw.fif",
    subject="sub-01",
)

Save only SNIRF

from shimadzu_fnirs_converter import convert_snirf

convert_snirf(
    txt_path="raw_data.TXT",
    origin_path="origin.csv",
    others_path="others.csv",
    out_snirf="sub01_raw.snirf",
    subject="sub-01",
)

Batch conversion

from shimadzu_fnirs_converter import convert_batch

jobs = [
    dict(
        txt_path="sub01.TXT",
        origin_path="origin.csv",
        others_path="others.csv",
        out_fif="sub01.fif",
        subject="sub-01",
    ),
    dict(
        txt_path="sub02.TXT",
        origin_path="origin.csv",
        others_path="others.csv",
        out_fif="sub02.fif",
        subject="sub-02",
    ),
]

convert_batch(jobs)

Command Line

shimadzu_fnirs_converter --help

Example:

shimadzu_fnirs_converter \
  --txt sub01_run1.TXT \
  --origin optodes_origin.csv \
  --others optodes_others.csv \
  --out sub01_raw.fif \
  --snirf sub01_raw.snirf \
  --subject sub-01

Requirements

• Python ≥ 3.9
• numpy ≥ 2.0
• pandas ≥ 2.0
• h5py ≥ 3.10
• mne ≥ 1.6

Citation

@software{dong2026shimadzu,
  author  = {Dong, Jiaran and Zhang, Jingyan and Feng, Chen},
  title   = {shimadzu_fnirs_converter: Shimadzu fNIRS TXT to SNIRF/FIF converter},
  year    = {2026},
  doi     = {10.5281/zenodo.18607367},
  url     = {https://doi.org/10.5281/zenodo.18607367}
}

License

MIT License

Authors

Jiaran Dong, Jingyan Zhang, Chen Feng