<!-- markdownlint-disable-file MD041 -->
[](https://hub.docker.com/r/flywheel/mriqc/)
[](https://hub.docker.com/r/flywheel/mriqc/)
# MRIQC Gear
## Overview
### Summary
*Image quality metrics for quality assessment of MRI. For more information
see [MRIQC's documentation](http://mriqc.readthedocs.io).*
### 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
- [x] Acquisition
- [ ] Analysis
----
[[*TOC*]]
----
### 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](https://mriqc.readthedocs.io/en/latest/reports/smri.html#verbose-reports).*
- __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*.
1. __*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*.
1. __*Measurement*__
- Location: *Information.Modality(MR - Magnetic Resonance).Measurement*
- Level: *File*
- Note: *Only required when gear is run in "auto-detect" mode*.
Raw data
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"description": "<!-- markdownlint-disable-file MD041 -->\n[](https://hub.docker.com/r/flywheel/mriqc/)\n[](https://hub.docker.com/r/flywheel/mriqc/)\n\n# MRIQC Gear\n\n## Overview\n\n### Summary\n\n*Image quality metrics for quality assessment of MRI. For more information\nsee [MRIQC's documentation](http://mriqc.readthedocs.io).*\n\n### Cite\n\n*Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ; MRIQC:\nAdvancing the Automatic Prediction of Image Quality in MRI from Unseen Sites;\nPLOS ONE 12(9):e0184661; doi:10.1371/journal.pone.0184661.*\n\n### License\n\n*License:* *BSD-3-Clause*\n\n### Classification\n\n*Category:* *QA (Utility)*\n\n*Gear Level:*\n\n- [ ] Project\n- [ ] Subject\n- [ ] Session\n- [x] Acquisition\n- [ ] Analysis\n\n----\n\n[[*TOC*]]\n\n----\n\n### Inputs\n\n- *nifti*\n - __Type__: *NIfTI file (.nii, .nii.gz)*\n - __Optional__: *False*\n - __Description__: *MRI NIfTI file. Input can be a structural image (T1, T2) or a\n functional NIfTI file.*\n - __Notes__: *Intent and Measurement classification fields must be present in the\n input metadata for 'auto-detect' mode to work.*\n\n### Config\n\n- *debug*\n - __Type__: *boolean*\n - __Description__: *Log debug messages*\n - __Default__: *False*\n\n- *measurement*\n - __Type__: *\"enum\": [\"auto-detect\", \"functional\", \"T1\", \"T2\"]*\n - __Description__: *Measurement of the input image. Note: for \"auto-detect\" mode to work,\n the input niftimust have the Intent and Measurement classification fields present in\n its metadata.*\n - __Default__: *\"auto-detect\"*\n\n- *verbose_reports*\n - __Type__: *boolean*\n - __Description__: *Produce [verbose report outputs](https://mriqc.readthedocs.io/en/latest/reports/smri.html#verbose-reports).*\n - __Default__: *False*\n\n- *include_rating_widget*\n - __Type__: *boolean*\n - __Description__: *Include the MRIQC built-in rating widget (does not function in flywheel).*\n - __Default__: *False*\n\n- *tag*\n - __Type__: *string*\n - __Description__: *Tag to add to the input file.*\n - __Default__: *mriqc*\n\n- *save_derivatives*\n - __Type__: *boolean*\n - __Description__: *Save the derivative JSON file generated by MRIQC algorithm.\n - __Note__: The metrics produced in this document are saved as custom metadata to\n the input file regardless of whether this JSON is saved.\n - __Default__: *false*\n\n### Outputs\n\n#### Files\n\n- *Report*\n - __Description__: *Zipped html archive. Contains .html report and .svg images.*\n - __Notes__: *Archive is viewable in Flywheel.*\n - __Optional__: *False*\n\n- *Derivative JSON*\n - __Description__: *JSON file containing image quality metrics (IQM).*\n - __Notes__: *Only saved when 'save_derivatives' config option set to True.*\n - __Optional__: *True*\n\n#### Metadata\n\nImage quality metrics (IQM) are saved to the input nifti file as Custom\nInformation fields, located under the \"derived.IQM\" keys.\n\n### Pre-requisites\n\n#### Prerequisite Metadata\n\n1. __*Modality*__\n - Location: *Information*\n - Level: *File*\n - Note: *Must be MR - Magnetic Resonance*.\n - Note: *Only required when gear is run in \"auto-detect\" mode*.\n\n1. __*Intent*__\n - Location: *Information.Modality(MR - Magnetic Resonance).Intent*\n - Level: *File*\n - Note: *Must be Structural or Functional*.\n - Note: *Only required when gear is run in \"auto-detect\" mode*.\n\n1. __*Measurement*__\n - Location: *Information.Modality(MR - Magnetic Resonance).Measurement*\n - Level: *File*\n - Note: *Only required when gear is run in \"auto-detect\" mode*.\n",
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