MRSIPrep

Getting Started:

  • Installation
    • Option A: plain docker run
    • Option B: the mrsiprep-docker wrapper
    • Minimum hardware requirements
    • Container internals
  • Basic Usage
    • Try it now: demo on the public SynthMRSI-Project dataset
    • The Nipype workflow engine
    • Verbosity, logging, and provenance
      • Per-recording logbook and provenance
    • Tissue backends (parc-con mode)
    • Command-Line Arguments
      • Positional Arguments
      • Options for filtering BIDS queries
      • quality thresholds
      • T1 saturation correction
      • Options for performing only a subset of the workflow
      • Specific options for registrations
      • parcellation
      • connectivity
      • Workflow configuration
      • overwrite/recompute
      • Other options
    • Output layout
    • BIDS import utilities
    • Limitations and scope
    • Troubleshooting
  • MNI Normalization Usage
    • ANTs-SyN normalization
  • Longitudinal (Subject-Template) Normalization
    • Algorithm
    • Execution order and caching
    • Derivatives
    • Preflight status
  • Parcellation and Connectivity Usage
    • Chimera parcellation
    • Bundled MNI atlas
    • Regional metabolic profiles and connectivity
  • T1 Saturation Correction
    • Requirements
    • Currently supported metabolites
    • Water-referencing status
    • Outputs

Benchmarks:

  • Runtime Benchmarks
    • Hardware
      • Compute (this benchmark)
      • MRI scanners
    • MRSI Acquisition: ECCENTRIC
      • Metabolite acquisition
      • Water reference
      • Reconstruction and quantification
    • MRSIPrep Benchmark Method
      • Resolution and useful-voxel counts
    • Results
    • Interpretation
    • Registration Frameworks
      • Method
      • Results
      • Conclusions
  • Voxel-Based Detection Benchmark
    • Dataset
      • Spike filter interaction
      • Runs compared
    • Injection regions
    • Detection results by backend
    • ROC / Precision-Recall curves
      • Interpretation
    • GM-precise boundary tracking (CrPCr / Precuneus only)
      • GM-only region source
      • Detection vs. the GM-precise ground truth
      • Boundary-distance metric
      • Interpretation
  • Cross-Site/Cross-Sequence Regional Profile Reproducibility
    • Dataset
    • Method
    • Results

Developer Reference:

  • API Reference
    • Configuration
      • mrsiprep.config.settings
      • mrsiprep.config.defaults
    • Top-level orchestration
      • mrsiprep.workflows.participant
      • mrsiprep.workflows.base
    • Pipeline stage workflows
      • mrsiprep.workflows.anatomical
      • mrsiprep.workflows.mrsi
      • mrsiprep.workflows.tissue
      • mrsiprep.workflows.registration
      • mrsiprep.workflows.parcellation
      • mrsiprep.workflows.connectivity
      • mrsiprep.workflows.reports
    • Registration
      • mrsiprep.registration.mrsi_to_t1
      • mrsiprep.registration.t1_to_mni
      • mrsiprep.registration.subject_template
      • mrsiprep.registration.transforms
    • Backend interfaces
      • mrsiprep.interfaces.ants
      • mrsiprep.interfaces.fsl
      • mrsiprep.interfaces.freesurfer
      • mrsiprep.interfaces.chimera
    • MRSI processing
      • mrsiprep.mrsi.filtering
      • mrsiprep.mrsi.masks
      • mrsiprep.mrsi.quality
      • mrsiprep.mrsi.reference
      • mrsiprep.mrsi.resampling
      • mrsiprep.mrsi.pvc
    • Tissue segmentation
      • mrsiprep.tissue.synthseg_fast
      • mrsiprep.tissue.fuzzy_cmeans
      • mrsiprep.tissue.fractions
      • mrsiprep.tissue.psf
    • Parcellation and connectivity
      • mrsiprep.parcellation.synthseg
      • mrsiprep.parcellation.chimera_native
      • mrsiprep.parcellation.mni_atlas
      • mrsiprep.parcellation.extraction
      • mrsiprep.parcellation.tissue_regression
      • mrsiprep.connectivity.export
      • mrsiprep.connectivity.connectivity
    • I/O
      • mrsiprep.io.bids
      • mrsiprep.io.loaders
      • mrsiprep.io.naming
      • mrsiprep.io.derivatives
      • mrsiprep.io.validators
      • mrsiprep.io.mrsinmrs
  • Changelog
    • 1.9.1
    • 1.9.0
    • 1.8.0
    • 1.7.6
    • Unreleased (previous)
    • 0.1.0
MRSIPrep
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© Copyright 2026, Federico Lucchetti.

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