Welcome to MRIQC’s documentation!
MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
MRIQC is an open-source project, developed under the following software engineering principles:
Modularity and integrability: MRIQC implements a nipype workflow to integrate modular sub-workflows that rely upon third party software toolboxes such as ANTs and AFNI.
Minimal preprocessing: the MRIQC workflows should be as minimal as possible to estimate the IQMs on the original data or their minimally processed derivatives.
Interoperability and standards: MRIQC follows the the brain imaging data structure (BIDS), and it adopts the BIDS-App standard.
Reliability and robustness: the software undergoes frequent vetting sprints by testing its robustness against data variability (acquisition parameters, physiological differences, etc.) using images from OpenfMRI. Its reliability is permanently checked and maintained with CircleCI.
Citation
Support and communication
The documentation of this project is found here: https://mriqc.readthedocs.io/.
Users can get help using the mriqc-users google group.
All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/nipreps/mriqc/issues.
Development
A local development build based on the latest docker build of MRIQC can be built with this command run from the root of this repository:
docker build -f Dockerfile_devel -t mriqc_devel .
To test changes the local source code will need to be mounted into the development container:
docker run --rm -v .:/src/mriqc mriqc_devel
New Python dependencies can be added in pyproject.toml
under dependencies
.
Any time a dependency is changed or added there the docker image will need to be rebuilt
using the above docker build
command.
License information
MRIQC adheres to the general licensing guidelines of the NiPreps framework.
MRIQC originally derives from, and hence is heavily influenced by, the
PCP Quality Assessment Protocol.
Please check the NOTICE
file for further information.
License
Copyright (c) 2021, the NiPreps Developers.
As of the 21.0.x pre-release and release series, MRIQC is licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Acknowledgements
This work is steered and maintained by the NiPreps Community. The development of this resource was supported by the Laura and John Arnold Foundation (RAP and KJG), the NIBIB (R01EB020740, SSG; 1P41EB019936-01A1SSG, YOH), the NIMH (RF1MH121867, RAP, OE; R24MH114705 and R24MH117179, RAP; 1RF1MH121885 SSG), NINDS (U01NS103780, RAP), and NSF (CRCNS 1912266, YOH). OE acknowledges financial support from the SNSF Ambizione project “Uncovering the interplay of structure, function, and dynamics of brain connectivity using MRI” (grant number PZ00P2_185872).
Contents
- Introduction
- Installation
- Running MRIQC
- About the NiPreps framework licensing
- Run mriqc with docker
- Image Quality Metrics (IQMs)
- Visual Reports
- Workflows
- Data Sharing Agreement
- About the NiPreps framework licensing
- What’s new
- 24.0.2 (August 26, 2024)
- 24.0.1 (August 20, 2024)
- 24.0.0 (April 17, 2024)
- 23.1.1 (March 20, 2024)
- 23.1.0 (June 14, 2023)
- 23.0.1 (March 24, 2023)
- 23.0.0 (March 10, 2023)
- 22.0.6 (August 24, 2022)
- 22.0.5 (August 24, 2022)
- 22.0.4 (August 23, 2022)
- 22.0.3 (August 19, 2022)
- 22.0.2 (August 15, 2022)
- 22.0.1 (May 3rd, 2022)
- 22.0.0 (May 3rd, 2022)
- Series 0.16.x
- Older (unsupported) series
- 0.15.3 (September 18, 2020)
- 0.15.2 (April 6, 2020)
- 0.15.1 (July 26, 2019)
- 0.15.0 (April 5, 2019)
- 0.14.2 (August 20, 2018)
- 0.14.1 (August 20, 2018)
- 0.14.0 (August 17, 2018)
- 0.13.1 (August 16, 2018)
- 0.13.0 (August 15, 2018)
- 0.12.1 (August 13, 2018)
- 0.12.0 (August 09, 2018)
- 0.11.0 (June 05, 2018)
- 0.10.6 (May 29, 2018)
- 0.10.5 (May 28, 2018)
- 0.10.4 (March 22, 2018)
- 0.10.3 (February 26, 2018)
- 0.10.2 (February 15, 2018)
- 0.10.1
- 0.9.10
- 0.9.9
- 0.9.8
- 0.9.7
- 0.9.6
- 0.9.5
- 0.9.4
- Release 0.9.3
- Release 0.9.2
- Release 0.9.1
- Release 0.9.0-2
- Release 0.9.0-1
- Release 0.9.0-0
- Release 0.8.9
- Release 0.8.8
- Release 0.8.7
- Release 0.8.6
- Release 0.8.5
- Release 0.8.4
- Release 0.8.3
- Release 0.8.2
- Release 0.3.0
- Release 0.1.0
- Release 0.0.2
- Release 0.0.1