مورد إلكتروني
Step-by-step pipeline for segmenting enlarged perivascular spaces from 3D T2-weighted MRI ; Mild Stroke Study 3 structural pipeline
| العنوان: | Step-by-step pipeline for segmenting enlarged perivascular spaces from 3D T2-weighted MRI ; Mild Stroke Study 3 structural pipeline |
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| المؤلفون: | Valdés Hernández, Maria del C., Ballerini, Lucia, Glatz, Andreas, Aribisala, Benjamin S., Bastin, Mark E., Dickie, David Alexander, Duarte Coello, Roberto, Munoz Maniega, Susana, Wardlaw, Joanna M. |
| المساهمون: | MRC - Medical Research Council, UKRI - UK Research and Innovation, Age UK, Alzheimer's Research UK, Scottish Government, SINAPSE-SPIRIT, Mrs Gladys Row Fogo Charitable Trust, Galen and Hilary Weston Foundation, Fondation Leducq, Scottish Funding Council, The UK Stroke Association, Valdés Hernández, Maria |
| بيانات النشر: | University of Edinburgh. College of Medicine and Veterinary Medicine. Centre for Clinical Brain Sciences |
| سنة النشر: | 2023 |
| المجموعة: | Edinburgh DataShare (University of Edinburgh) |
| مصطلحات موضوعية: | MATLAB, pipeline, brain, segmentation, magnetic resonance imaging, perivascular spaces, white matter hyperintensities, software, freesurfer, FSL, white matter, brain cortex, basal ganglia, centrum semiovale, Mathematical and Computer Sciences::Computer Vision |
| جغرافية الموضوع: | UK, UNITED KINGDOM, start=2018-08-01, end=2023-01-05, scheme=W3C-DTF |
| الوصف: | This dataset contains the matlab code to parcellate the brain, and segment brain tissues, white matter hyperintensities, and perivascular spaces from magnetic resonance imaging (MRI) structural sequences acquired using research protocols. It assumes isotropic or nearly-isotropic T2-weighted of voxel size approximately 1 mm3 as the image space where the fluid attenuated inversion recovery (FLAIR) and T1-weighted images are co-registered beforehand. It also assumes the image data is organised in BIDS (https://bids.neuroimaging.ioTest/) format, and that the contents of the intracranial volume have been previously extracted (although this is not a requirement). The code is written in MATLAB, and invokes third-party software for parcellating the brain and generating tissue priors. The results from the brain parcellation, are used further to clean the initial results of tissue and lesion segmentation procedures, and generate the regions of interest for assessing the enlarged perivascular spaces (PVS). Rather than an end-to-end encapsulated software, the code is presented as a step-by-step pipeline starting by the brain parcellation (step 03), with comments justifying and explaining every block of operations, as well as alternatives, to facilitate its use. It was developed for the Mild Stroke Study 3 (PMID: 33817338), a clinical study aimed at studying contributing factors and clinical implications of small vessel disease dynamics in adults that suffered a mild-to-moderate stroke. As such, the pipeline deals with a large range and variety of vascular abnormalities present in a large number of adult brain MRI scans, and can be widely applicable. However, it is intended as a guidance that will need to be further tuned for a specific cohort, to facilitate reproducibility of our brain research results. |
| نوع الوثيقة: | software |
| وصف الملف: | application/zip; application/pdf |
| اللغة: | English |
| العلاقة: | Barnes A, Ballerini L, Valdés Hernández MDC, Chappell FM, Muñoz Maniega S, Meijboom R, Backhouse EV, Stringer MS, Duarte Coello R, Brown R, Bastin ME, Cox SR, Deary IJ, Wardlaw JM. Topological relationships between perivascular spaces and progression of white matter hyperintensities: A pilot study in a sample of the Lothian Birth Cohort 1936. Front Neurol. 2022 Aug 24;13:889884. doi:10.3389/fneur.2022.889884. PMID: 36090857; PMCID: PMC9449650.; Clancy U, Garcia DJ, Stringer MS, Thrippleton MJ, Valdés-Hernández MC, Wiseman S, Hamilton OK, Chappell FM, Brown R, Blair GW, Hewins W, Sleight E, Ballerini L, Bastin ME, Maniega SM, MacGillivray T, Hetherington K, Hamid C, Arteaga C, Morgan AG, Manning C, Backhouse E, Hamilton I, Job D, Marshall I, Doubal FN, Wardlaw JM. Rationale and design of a longitudinal study of cerebral small vessel diseases, clinical and imaging outcomes in patients presenting with mild ischaemic stroke: Mild Stroke Study 3. Eur Stroke J. 2021 Mar;6(1):81-88. doi:10.1177/2396987320929617. Epub 2020 Jun 5. PMID: 33817338; PMCID: PMC7995323.; Jochems ACC, Muñoz Maniega S, Clancy U, Jaime Garcia D, Arteaga C, Hewins W, Penman R, Hamilton OKL, Czechoń A, Backhouse EV, Thrippleton MJ, Stringer MS, Bastin ME, Valdés Hernández MDC, Wiseman S, Chappell FM, Doubal FN, Wardlaw JM. Associations of Peak-Width Skeletonized Mean Diffusivity and Post-Stroke Cognition. Life (Basel). 2022 Aug 31;12(9):1362. doi:10.3390/life12091362. PMID: 36143398; PMCID: PMC9504440.; https://doi.org/10.7488/ds/3029Test; Valdés Hernández, Maria del C.; Ballerini, Lucia; Glatz, Andreas; Aribisala, Benjamin S.; Bastin, Mark E.; Dickie, David Alexander; Duarte Coello, Roberto; Munoz Maniega, Susana; Wardlaw, Joanna M. (2023). Step-by-step pipeline for segmenting enlarged perivascular spaces from 3D T2-weighted MRI, 2018-2023 [software]. University of Edinburgh. College of Medicine and Veterinary Medicine. Centre for Clinical Brain Sciences. https://doi.org/10.7488/ds/7486Test.; https://hdl.handle.net/10283/8501Test; https://doi.org/10.7488/ds/7486Test |
| DOI: | 10.7488/ds/7486 |
| الإتاحة: | https://doi.org/10.7488/ds/7486Test https://doi.org/10.3389/fneur.2022.889884Test https://doi.org/10.1177/2396987320929617Test https://doi.org/10.3390/life12091362Test https://doi.org/10.7488/ds/3029Test https://hdl.handle.net/10283/8501Test |
| حقوق: | Creative Commons Attribution 4.0 International Public License |
| رقم الانضمام: | edsbas.5BE4EE47 |
| قاعدة البيانات: | BASE |
| DOI: | 10.7488/ds/7486 |
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