ChRIS- A web-based neuroimaging and informatics system for collecting, organizing, processing, visualizing and sharing of medical data

Abstract

The utility of web browsers for general purpose computing, long anticipated, is only now coming into fruition. In this paper we present a web-based medical image data and information management software platform called ChRIS ([Boston] Children's Research Integration System). ChRIS' deep functionality allows for easy retrieval of medical image data from resources typically found in hospitals, organizes and presents information in a modern feed-like interface, provides access to a growing library of plugins that process these data - typically on a connected High Performance Compute Cluster, allows for easy data sharing between users and instances of ChRIS and provides powerful 3D visualization and real time collaboration.

Brain morphological analysis in PTEN hamartoma tumor syndrome

“…All participants were imaged with clinical 3T MRI scanners (MAGNETOM Skyra, Siemens Medical Systems, Erlangen, Germany) at BCH. DICOM files of 3D T1‐weighted MPRAGE (TR 2,000–2,520 ms; TE 1.7–2.6 ms, voxel size 0.52–1.0 × 0.52–1.0 × 0.9–1.0 mm, matrix 256 × 256) were accessed through the Children's Research and Integration System (Pienaar, Rannou, Bernal, Hahn, & Grant, ), and analyzed with CIVET version 2.1.0 pipeline (Zijdenbos, Forghani, & Evans, ) using CBRAIN platform (Sherif, Rioux, Rousseau, et al, ). The brain structural analysis using the CIVET pipeline included correction for intensity nonuniformity artifacts by the N3 algorithm (Sled, Zijdenbos, & Evans, ), nonlinear registration to a stereotaxic ICBM152 2009 template space (Fonov, Evans, McKinstry, Almli, & Collins, ), brain masking (Smith, ), tissue classification using an artificial neural network classifier (INSECT) (Tohka, Zijdenbos, & Evans, ; Zijdenbos et al, ), and brain segmentation using ANIMAL (Collins, Zijdenbos, Baaré, & Evans, ).…”

The left lateral occipital cortex exhibits decreased thickness in children with sensorineural hearing loss

“…DICOM files were collected through the Children's Research and Integration System (Pienaar et al, 2015), and analyzed with CIVET version 2.1.0 pipeline (Zijdenbos et al, 2002) on the CBRAIN platform (Sherif et al, 2015). Corrections for non‐uniform intensity artifacts by the N3 algorithm (Sled et al, 1998), stereotaxic registration (onto the icbm152 non‐linear 2009 template) (Fonov et al, 2009), and brain masking (Smith, 2002) were performed.…”

Surface‐ and voxel‐based brain morphologic study in Rett and Rett‐like syndrome with MECP2 mutation

“…Three-dimensional (3-D) T1-weighted MPRAGE images (TR 2000-2500 ms; TE 1.7-2.5 ms, voxel size 0.85-1 × 0.85-1 x 1 mm, matrix 256 × 256) were obtained from all participants included in this study with clinical 3 T MRI scanners (MAGNETOM Skyra, Siemens Medical Systems, Erlangen, Germany). DICOM files were collected through the Children's Research and Integration System (Pienaar et al, 2015), and analyzed with CIVET version 2.1.0 pipeline (Zijdenbos et al, 2002) on the CBRAIN platform (Sherif et al, 2014). Corrections for non-uniform intensity artifacts by the N3 algorithm (Sled et al, 1998), stereotaxic registration (onto the icbm152 non-linear 2009 template) (Fonov et al, 2009), and brain masking (Smith, 2002) were performed.…”