Tools
This page is meant to be a dynamic collection of various QC tools that are available, with a brief summary of their purpose, usage, outputs and the technology they are based on.
If you don't see your own tool or a tool that you think should belong here, please send a pull request (PR) with the changes needed, or open an issue at the niQC repo. Thank you for your contribution.
Table of Contents
Multimodal
| Tool/resource | Modalities | Interaction | Technology | Outputs |
|---|---|---|---|---|
| MRIQC | T1w, fMRI | Interactive & Automated | Python | Plots, reports, IQMs |
| VisualQC | Various modalities: T1wMRI, fMRI, DWI, Quantitative MR | Interactive | Python | Plots, reports |
Anatomical (T1w MRI etc)
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| braindr | T1w or other 2D slices, segmentation | Interactive | JavaScript | Plots, reports |
| CAT12 | Extract overall weighted image quality (IQR) | Interactive & Automated | Matlab | Plots, reports, automated rating, QC pages |
| MRIQC | Identify outliers, Annotate, Extract Image Quality Metrics (IQMs), Quality Prediction | Interactive & Automated | Python | Plots, reports, IQMs, automated rating |
| MindControl | Identify outliers, Annotate, Review anatomical accuracy, Edit and correct voxels | Interactive | Python, Javascript | |
| PALS | Checks orientation of stroke T1w MRI + lesion mask inputs, performs lesion correction, calculates lesion load, and automatically outputs QC pages | Interactive | Python | QC pages, reports |
| Qoala-T | Quality rating of FreeSurfer segmentation | Batch Processing | R, FreeSurfer | Qoala-T ratings (0-100), plot + csv file |
| VisualQC | Detect and rate artefacts, Accuracy of volumetric or suface segmentations, check alignment | Interactive | Pure Python | Plots, reports |
Functional MRI
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| dashQC | Visualize distributions of quality metrics, check outliers and alignment | Interactive | JavaScript | Plots, reports |
| MRIQC | Identify outliers, Annotate, Extract Image Quality Metrics (IQMs) | Interactive & Automated | Python | Plots, reports, IQMs |
| pyfMRIqc | Calculates various Image Quality Metrics (IQMs) | Batch-processing | Python | Plots, reports, IQMs |
| rtQC | Various aspects of QC for real-time fMRI | Interactive | Matlab, SPM12 | Plots, reports, regressors for denoising |
| VisualQC | Detect and rate artefacts, Accuracy of volumetric or suface segmentations, check alignment | Interactive | Pure python | Plots, reports |
Diffusion MRI
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| DTIprep | QC | Batch processing | C++ | |
| eddyqc | QC | batch processing | C (FSL) | JSON, PDF |
| ExploreDTI - sign up required, free for academic research | Visualization and quality assessment | Interactive | Matlab | TBA |
| VisualQC | Detect and rate various artefacts, check alignment | Interactive | Plots, reports |
Arterial Spin Labeling
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| ExploreASL | image processing and statistics of ASL | Batch processing | Matlab/SPM | TBA |
Scanner and Hardware QC
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| UniQC | Unified QC of MRI sequence development and fMRI artefacts | Interactive | Matlab/SPM | Plots, interactive Matlab Image objects |
| mrQA | Automatic evaluation of protocol compliance | Automated | Python | Reports |
Miscellaneous
| Tool | Purpose | Interaction | Technology | Outputs |
|---|---|---|---|---|
| braindr | T1w or other 2D slices, segmentation | Interactive | JavaScript | Plots, reports |
| MRIQC Web-API | Crowdsource Image Quality Metrics (IQMs) | Automated | Database | IQMs & Expert quality annotations |
| ReproStim | Auto-collect audio/video stimuli as presented to participant | Automated | Magewell USB Capture Plus device | audio/video recording (BIDS) |