fw-gear-mriqc 0.9.0

Image quality metrics for quality assessment of MRI

MRIQC Gear

Overview

Summary

Image quality metrics for quality assessment of MRI. For more information see MRIQC's documentation.

Cite

Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ; MRIQC: Advancing the Automatic Prediction of Image Quality in MRI from Unseen Sites; PLOS ONE 12(9):e0184661; doi:10.1371/journal.pone.0184661.

License

License: BSD-3-Clause

Classification

Category: QA (Utility)

Gear Level:

• Project
• Subject
• Session
• Acquisition
• Analysis

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[[TOC]]

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Inputs

• nifti
  • Type: NIfTI file (.nii, .nii.gz)
  • Optional: False
  • Description: MRI NIfTI file. Input can be a structural image (T1, T2) or a functional NIfTI file.
  • Notes: Intent and Measurement classification fields must be present in the input metadata for 'auto-detect' mode to work.

Config

• debug

  • Type: boolean
  • Description: Log debug messages
  • Default: False

• measurement

  • Type: "enum": ["auto-detect", "functional", "T1", "T2"]
  • Description: Measurement of the input image. Note: for "auto-detect" mode to work, the input niftimust have the Intent and Measurement classification fields present in its metadata.
  • Default: "auto-detect"

• verbose_reports

  • Type: boolean
  • Description: Produce verbose report outputs.
  • Default: False

• include_rating_widget

  • Type: boolean
  • Description: Include the MRIQC built-in rating widget (does not function in flywheel).
  • Default: False

• tag

  • Type: string
  • Description: Tag to add to the input file.
  • Default: mriqc

• save_derivatives

  • Type: boolean
  • Description: *Save the derivative JSON file generated by MRIQC algorithm.
  • Note: The metrics produced in this document are saved as custom metadata to the input file regardless of whether this JSON is saved.
  • Default: false

Outputs

Files

• Report

  • Description: Zipped html archive. Contains .html report and .svg images.
  • Notes: Archive is viewable in Flywheel.
  • Optional: False

• Derivative JSON

  • Description: JSON file containing image quality metrics (IQM).
  • Notes: Only saved when 'save_derivatives' config option set to True.
  • Optional: True

Metadata

Image quality metrics (IQM) are saved to the input nifti file as Custom Information fields, located under the "derived.IQM" keys.

Pre-requisites

Prerequisite Metadata

1. Modality

   • Location: Information
   • Level: File
   • Note: Must be MR - Magnetic Resonance.
   • Note: Only required when gear is run in "auto-detect" mode.

2. Intent

   • Location: Information.Modality(MR - Magnetic Resonance).Intent
   • Level: File
   • Note: Must be Structural or Functional.
   • Note: Only required when gear is run in "auto-detect" mode.

3. Measurement

   • Location: Information.Modality(MR - Magnetic Resonance).Measurement
   • Level: File
   • Note: Only required when gear is run in "auto-detect" mode.