QRATER: a collaborative and centralized imaging quality control web-based application

Abstract

Quality control (QC) is an important part of all scientific analyses, including neuroscience. With manual curation considered the gold standard, there remains a lack of available tools that make manual neuroimaging QC accessible, fast, and easy. In this article we present Qrater, a containerized web-based Python application that enables viewing and rating any type of image for QC purposes. Qrater functionalities allow collaboration between various raters on the same dataset which can facilitate completing large QC tasks. Qrater was used to evaluate QC rater performance on three different magnetic resonance (MR) image QC tasks by a group of raters having different amounts of experience. The tasks included QC of raw MR images (10,196 images), QC of linear registration to a standard template (10,196 images), and QC of skull segmentation (6,968 images). We measured the proportion of failed images, average rating time per image, intra- and inter-rater agreement, as well as the comparison against QC using a conventional method. The median time spent rating per image differed significantly between raters (depending on rater experience) in each of the three QC tasks. Evaluating raw MR images was slightly faster using Qrater than an image viewer (expert: 99 vs. 90 images in 63 min; trainee 99 vs 79 images in 98 min). Reviewing the linear registration using Qrater was twice faster for the expert (99 vs. 43 images in 36 min) and three times faster for the trainee (99 vs. 30 images in 37 min). The greatest difference in rating speed resulted from the skull segmentation task where the expert took a full minute to inspect the volume on a slice-by-slice basis compared to just 3 s using Qrater. Rating agreement also depended on the experience of the raters and the task at hand: trained raters’ inter-rater agreements with the expert’s gold standard were moderate for both raw images (Fleiss’ Kappa = 0.44) and linear registration (Fleiss’ Kappa = 0.56); the experts’ inter-rater agreement of the skull segmentation task was excellent (Cohen’s Kappa = 0.83). These results demonstrate that Qrater is a useful asset for QC tasks that rely on manual evaluation of QC images.