gif
Module: mqc/gif
generates quality control (QC) screenshots between two MRI volumes or, if you give only one input, runs through all the images in a volume in 4d. It extracts the central sections (sagittal, coronal and axial) of the volumes, creates annotated mosaics and combines them into an animated GIF for rapid visual comparison.
Keywords : mqc, Visualisation, gif
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| image1 | file | first image to be analysed, either to be compared with the second, or to be analysed across the whole set of images, in which case you need to be in 4d. | *.{nii,nii.gz} | |
| image2 | file | seconde image to be analysed. | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| mqc_screenshots | file | .gif file containing quality control image for visually compares MRI volumes using middle-slice mosaics. | *_screenshots_merged_mqc.gif |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
| MRtrix3 | MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging. | |
| imagemagick | ImageMagick is a free, open-source software suite, used for editing and manipulating digital images. |
Authors
Last updated : 2025-07-15