neuroops 0.3.0

A linter for neuroimaging data + universal format converter to BIDS

🧠 NeuroOps

A linter for neuroimaging data + universal format converter to BIDS

Installation • Quick Start • Converter • Checks

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Problem 1: Your fMRIPrep run fails at 3am because the input was a renamed DICOM.

Problem 2: You have 50 EDF files to convert to BIDS. It takes 2 weeks of scripting.

NeuroOps solves both.

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Installation

pip install neuroops

For EEG format conversion:

pip install neuroops[convert]

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Quick Start

Lint a file

neuroops check scan.nii.gz

🔍 Linting: scan.nii.gz
  ✅ gzip_magic: Valid gzip compression
  ✅ magic_bytes: Valid NIfTI header
  ✅ orientation_codes: Orientation defined
  ✅ snr: SNR = 8.2
  
✅ Result: PASS

Convert to BIDS

neuroops convert recording.edf -o ./bids -s 01 -t rest

✅ Conversion successful!
   Output: ./bids/sub-01/eeg/sub-01_task-rest_eeg.edf
   Format: .edf → BIDS

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Format Converter

Convert any format to BIDS with one command. Saves 2+ weeks of scripting.

# Single file
neuroops convert recording.edf --output ./bids --subject 01 --task rest

# Batch convert folder
neuroops convert ./raw_data/ --output ./bids --subject 01 --batch

Supported formats

Format	Extension
EDF	.edf
BDF	.bdf
EEGLAB	.set
BrainVision	.vhdr
Elekta/Neuromag	.fif
NIfTI	.nii, .nii.gz
DICOM	.dcm, folder

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What It Catches

Pipeline Killers

Problem	Detection
Fake .gz file	Checks 1f 8b magic bytes
Corrupted header	Validates NIfTI magic
Zero-byte file	Size check
NaN in affine	Matrix validation

Silent Killers

Problem	Detection
TR mismatch	NIfTI header vs JSON sidecar
Missing orientation	sform/qform code check
3D in func/	Dimension validation
Orphan sidecars	File pairing check

Quality Warnings

Check	Default
SNR	> 5.0
Motion	< 2.0 voxels
Dropout	< 15% zeros
Ghost	< 5% background

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CLI Reference

neuroops check file.nii.gz                    # Lint single file
neuroops check file.nii.gz --allow-abnormalities  # Skip anatomy checks
neuroops scan ./dataset                       # Lint directory

neuroops convert file.edf -o ./bids -s 01 -t rest  # Convert to BIDS
neuroops convert ./folder -o ./bids -s 01 --batch  # Batch convert

Exit Code	Meaning
0	PASS
1	WARN
2	FAIL

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Python API

from neuroops.validation import IntegrityChecker
from neuroops.converter import FormatConverter

# Lint
checker = IntegrityChecker()
results = checker.run_all_checks("scan.nii.gz")

# Convert
converter = FormatConverter()
result = converter.to_bids("recording.edf", "./bids", subject="01", task="rest")

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License

MIT