- 👀 This repository contains supporting code & data (below) for the published articles.
- 👀 You will find here also packages (below) related to diffusion MRI or histology analysis.
- Coregistration between histology and MR images (rigid and non-rigid landmark based and rigid coregistration of two histology slides).
- Convolutional neural network analysis of histology slides.
- Structure tensor analysis of histology slides.
- Graphical User interface.
- Monte Carlo simulator of diffusion in 1D-pathways with their diffusion spectra and dMRI signal.
- Semi-analytical simulator of diffusion in 1D-pathways with their diffusion spectra and diffusion MRI signal.
- Analytical prediction for diffusion spectrum of restrictive diffusion between planes, in a circle or a sphere.
- Functions supporting diffusion spectrum analysis according to Stepisnik et al. 1993.
- Functions supporting generation of diffusion MRI signal from simulated diffusion.
- Histogram analysis within region-of-interests.
- Plotting function used in published peer-reviewd articles [1], [2], [3], [4], [5].
- Code related to the dissertation.
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Brabec, J., Englund, E., Bengzon, J., Szczepankiewicz, F., Van Westen, D., Sundgren, P.C. and Nilsson, M., 2023. Coregistered histology sections with diffusion tensor imaging data at 200 µm resolution in meningioma tumors. Data in Brief, 48, p.109261. -[GitHub]-[Article in HTML]-[Article in PDF]-
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Brabec, J., Friedjungova, M., Vašata, D., Englund, E., Bengzon, J., Knutsson, L., Szczepankiewicz, F., van Westen, D., Sundgren, P.C. and Nilsson, M., 2023. Meningioma microstructure assessed by diffusion MRI: an investigation of the source of mean diffusivity and fractional anisotropy by quantitative histology. NeuroImage: Clinical, p.103365. -[GitHub]-[Article in HTML]-[Article in PDF]-
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Brabec, J., Durmo, F., Szczepankiewicz, F., Brynolfsson, P., Lampinen, B., Rydelius, A., Knutsson, L., Westin, C.F., Sundgren, P.C. and Nilsson, M., 2022. Separating Glioma Hyperintensities From White Matter by Diffusion-Weighted Imaging With Spherical Tensor Encoding. Frontiers in Neuroscience, 16. -[GitHub]-[Article in HTML]-[Article in PDF]-
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Brabec, J., Szczepankiewicz, F., Lennartsson, F., Englund, E., Pebdani, H., Bengzon, J., Knutsson, L., Westin, C.F., Sundgren, P.C. and Nilsson, M., 2022. Histogram analysis of tensor-valued diffusion MRI in meningiomas: Relation to consistency, histological grade and type. NeuroImage: Clinical, 33, p.102912. -[GitHub]-[Article in HTML]-[Article in PDF]-
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Brabec, J., Lasič, S. and Nilsson, M., 2020. Time‐dependent diffusion in undulating thin fibers: Impact on axon diameter estimation. NMR in Biomedicine, 33(3), p.e4187. -[GitHub]-[Article in HTML]-[Article in PDF]-
For other articles, please see Google Scholar or ResearchGate.
- 👋 I am @jan-brabec and I am interested in diffusion MRI.
- 👀 I am a post-doc at John Hopkins University, USA.
- 👀 Background: Post-doc at John Hopkins university, USA; PhD in diffusion MRI and Master in Science in Physics both from Lund University in Sweden; M.D. from Masaryk University in Brno in the Czech Republic.
- 👀 Website, Google Scholar, ResearchGate, Linkedin
- 📫 E-mail: brabec [at] kennedykrieger [dot] org
All work under 