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

`Input 1`

Format : tuple val(meta), path(image1), path(image2)

	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.	True	`*.{nii,nii.gz}`
image2	file	Second image to be analysed.	False	`*.{nii,nii.gz}`

Outputs

`mqc_screenshots`

Format : tuple val(meta), path(*_screenshots_merged_mqc.gif)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	True
*_screenshots_merged_mqc.gif	file	.gif file containing quality control image for visually compares MRI volumes using middle-slice mosaics.	True	`*_screenshots_merged_mqc.gif`

`versions`

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	`versions.yml`

Arguments (see process.ext)

	Type	Description
title_image1	string	name given to the first image
title_image2	string	name given to the second image
suffix_qc	string	suffix given to final image

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.	10.1016/j.neuroimage.2019.116137
imagemagick	ImageMagick is a free, open-source software suite, used for editing and manipulating digital images.

Authors

@ThoumyreStanislas

Last updated : 2025-10-30