DOI: 10.7488/ds/7454
title: Measurements of a perivascular spaces magnetic resonance imaging physical phantom and correspondent digital reference object model
title: Perivascular spaces magnetic resonance imaging physical and digital phantoms

description: Magnetic Resonance Imaging (MRI) visible perivascular spaces (PVS) have been associated with age, decline in cognitive abilities, interrupted sleep, and markers of small vessel disease. Therefore, several computational methods have been developed for their assessment from brain MRI. But the limits of validity of these methods under various spatial resolutions, and the accuracy in detecting and measuring the dimensions of these structures have not been established. We developed a digital object identifier (DRO) and validated it using a physical phantom from UMC Utrecht to answer these questions. Our in-silico phantom or PVS-DRO consist on cylinders with varying diameters from 0.2 to 3mm each one confined to a space of 15x15x15 mm as per “enlarged MRI-visible PVS” are defined in the literature. This dataset contains the source code to generate such in-silico cylinders, an excel spreadsheet with the measurements of the cylinders of the UMC Utrecht physical phantom from thresholding the output of two vesselness filters: Frangi and RORPO, and the source code to generate such measurements. The excel file also contains Bland-Altman analyses to inform on the accuracy and behaviour of the filters in scenarios of varying spatial resolution and cylinders’ orientation. The file relates to the upcoming publication Duarte Coello, R., Valdés Hernández, M.C., Zwanenburg, J.J.M., van der Velden, M., Kuijf, H.J., De Luca, A., Bernal Moyano, J., Ballerini, L., Chappell, F.M., Brown, R., Biessels, G.J., Wardlaw, J.M. (in submission). "On the detectability and accuracy of computational measurements of enlarged perivascular spaces from magnetic resonance images".
description: Data Files 1) Compressed file PVS_DRO_code.gz Contains the matlab files Example.m and PVS_cylinder.m. Example.m is an example script to generate a cylinder using the function PVS_cylinder, which is implemented in PVS_cylinder.m 2) Compressed file UMC_Utrecht_Phantom_Code.gz Contains the matlab files to generate the measurements in the spreadsheet and their output. The README file indicates the two external libraries needed to run the scripts. Names are self-explanatory. To generate the diameters obtained from scanning the phantom in different orientations, the corresponding scripts are named Process_phantom_orientation_FRANGI.m and Process_phantom_orientation_RORPO.m. For generating the diameters at different voxel sizes, the scripts are Process_phantom_resolution_RORPO.m and Process_phantom_resolution_FRANGI.m. For filtering using RORPO as implemented in the code provided by the developers, the function RORPO_multiscale developed in-house (RORPO_multiscale.m, provided in this dataset) is used. The datasets processed by the code (i.e., physical phantom images in nifti.gz format), to evaluate effect of different orientations and voxel sizes in the measurements, are provided in the respective folders. Original dicom files and technical specifications of the physical phantom are not part of this dataset, and are hosted by the Imaging Sciences Institute and Center at UMC Utrecht. The matlab function anisotropic_correction, which corrects the individual PVS measurements considering anisotropic voxels, and is implemented in the matlab file anisotropic_correction.m, is used by the processing scripts to compute the PVS dimensions. 3) Physical_phantom_results.xlsx Contains 12 worksheets, pertinent to measurements in the physical phantom from UMC Utrecht, which consists on a Perspex plate with holes of diameters ranging from 0.2 to 3 mm, filled with water and scanned with a T2-weighted contrast using a turbo spin-echo sequence in a 7T Phillips MRI scanner. 4) Readme file explaining the contents of each file and data worksheet in detail