Unverified Commit cabbd430 authored by Arvid Lundervold's avatar Arvid Lundervold Committed by GitHub

Update README.md

parent 0a8fe09b
......@@ -54,12 +54,12 @@ Throughout the course you will work with notebooks that contain various material
- **[Lec 0](https://docs.google.com/presentation/d/1aoNyjXZ053yCUbdY5YVAtftGL2yym10QmbnnrlNFr7A/edit?usp=sharing): Course overview; [SW installation](setup.md); Motivation:** [Can a biologist fix a radio?](https://www.cell.com/cancer-cell/pdf/S1535-6108(02)00133-2.pdf) Lazebnic (2002); [Why programming?](https://drive.google.com/file/d/1Zss5kTEgVmoF8PxQpho2yvfNviJOksgv); Why top-down? - [teaching "the whole game"](https://www.fast.ai/2016/10/08/teaching-philosophy) (see also https://computingskillsforbiologists.com)
- **[Lec 1](https://docs.google.com/presentation/d/1fZEID0NKFBdtMsQgzMuNwpvaUa-y7LAIihpap0Y3Q20/edit?usp=sharing)**: _Introduction to modelling, MRI, and image processing_; **BROWSE through**: [Tofts (2018) Ch. [1](https://drive.google.com/open?id=1s36p4vEXEEfmL3KZqMaHkbu4e58XMgDj), Ch. [2](https://drive.google.com/open?id=1zWhdLIzTFsk92a-XLWj7eW8pHmDs5VEG), Ch. [17](https://drive.google.com/open?id=19U76zBL2ZQrRnhUT-s_GpFzPM29WpJLB), Ch. [18](https://drive.google.com/open?id=1t9vUUJ6Xc4zmCdCjwNJuqhZHo_CV06ad); McRobbie (2017) Ch. [3](https://drive.google.com/open?id=1igDMEVAnWR3kU1doXTz_X-LygdVLQovJ), Ch. [4](https://drive.google.com/open?id=15_9lHA_6DXZHhQEXH2T-VLNDbV16A1zo), Ch. [5](https://drive.google.com/open?id=14TGT59koVT6ujgYNDwK5G5xOA3LFlcSI), Ch. [8](https://drive.google.com/open?id=1CiCRAslFUb5Q3DZqpbEhkdBJm57vQx4O)]
- **[Lec 2](https://docs.google.com/presentation/d/1qMxwu401az5zgq6Rg5M7kOtygdeosnMeSucvy7SSbNk/edit?usp=sharing)**: _Water diffusion_, dMRI, and tissue microstructure - Part 1 [Tofts (2018) Ch. [8](https://drive.google.com/open?id=1rck9B5qsW0uV49D9588HolNLCRm7g9jy); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 303-310.]
- **[Lec 2](https://docs.google.com/presentation/d/1qMxwu401az5zgq6Rg5M7kOtygdeosnMeSucvy7SSbNk/edit?usp=sharing)**: _Water diffusion_, dMRI, and tissue microstructure - Part 1 [Tofts (2018) Ch. [8](https://drive.google.com/open?id=1rck9B5qsW0uV49D9588HolNLCRm7g9jy); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 303-310]. Video recording from the dMRI session: https://youtu.be/ZkVclYejv54
- **[Lec 3](https://docs.google.com/presentation/d/1pcFZO9H3EOrB3rYgUuIjd9Ja_UfMWjULH8wSZcOYDbw/edit?usp=sharing)**: _Water diffusion_, diffusion tensor imaging and beyond - Part 2 [Tofts (2018) Ch. [9](https://drive.google.com/open?id=1ZRfd4iI8q0VmfuEzPVwgkhlHawvrglf3); [Westin (2002)](https://drive.google.com/open?id=1WkAbJi3Xh4sdDdBMiu9yuXEU9UzGKKSs)]
- **[Lec 4](https://docs.google.com/presentation/d/1C0WGl1qKrQdwrMKOMfWyTnnASLzECRKhvLhZozphJwQ/edit?usp=sharing)**: _Blood perfusion_ and dynamic susceptibility contrast MRI (DSC-MRI) - Part 1 [Tofts (2003) Ch. [11](https://drive.google.com/open?id=1DWhL0B8xGc1EL1Ag7J4I2iCMBdHl-2mA); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 311-314.]
- **[Lec 5](https://docs.google.com/presentation/d/1CTuA2tBCBQaWHL7_k2o0o26E8Lp6G4UaNjlL1y2Qsac/edit?usp=sharing)**: _Blood perfusion_, tracer kinetics, and deconvolution - Part 2 [Tofts (2003) Ch. [11](https://drive.google.com/open?id=1DWhL0B8xGc1EL1Ag7J4I2iCMBdHl-2mA)]
- **[Lec 6](https://docs.google.com/presentation/d/1EYuKHtQM4RIgkvIxrMyAkq02l8KUd9WuCsjCHviBaKI/edit?usp=sharing)**: _Vascular permeability_, compartment modelling, and T1w dynamic contrast-enhanced MRI (DCE-MRI) [Tofts (2018) Ch. [14](https://drive.google.com/open?id=1Wy6ZGurLkV18q6v1XAlhMRfvLttV2f08); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 316-319; Measurement of Renal Perfusion and Filtration with MRI [GitHub](https://github.com/arvidl/functional-kidney-imaging) / [slides](https://docs.google.com/presentation/d/1WS6ODHrXOfYL-fXLw847EkYR4qcvDJA6bRTvqFE_fIY/edit?usp=sharing)] Video recording from this session: https://youtu.be/X4zGyhid48U
- **[Lec 7](https://docs.google.com/presentation/d/142Y5wQKkIvRkcmBiSV2INDhuMdRHrpPhxqs2zx17ZCY/edit?usp=sharing)**: _Brain connectivity_ assessed with aMRI, dMRI, fMRI and network (graph) theory [Fornito (2016) Ch. [1](https://drive.google.com/open?id=179E3CAZsV6LzV7Jb37eHmczuzVLJUB4H); [Bassett (2018)](https://drive.google.com/open?id=1PW30HroQMBLPLDiZsnhJZ-obumW5RaEA); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 319-325.] Video recording from this session: https://youtu.be/rAbNbpcUNdY
- **[Lec 4](https://docs.google.com/presentation/d/1C0WGl1qKrQdwrMKOMfWyTnnASLzECRKhvLhZozphJwQ/edit?usp=sharing)**: _Blood perfusion_ and dynamic susceptibility contrast MRI (DSC-MRI) - Part 1 [Tofts (2003) Ch. [11](https://drive.google.com/open?id=1DWhL0B8xGc1EL1Ag7J4I2iCMBdHl-2mA); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 311-314]. Video recording from this session: https://youtu.be/h1AboyMq7Uw
- **[Lec 5](https://docs.google.com/presentation/d/1CTuA2tBCBQaWHL7_k2o0o26E8Lp6G4UaNjlL1y2Qsac/edit?usp=sharing)**: _Blood perfusion_, tracer kinetics, and deconvolution - Part 2 [Tofts (2003) Ch. [11](https://drive.google.com/open?id=1DWhL0B8xGc1EL1Ag7J4I2iCMBdHl-2mA)]. Video recording from thos session: https://youtu.be/mTCs2MFxEzk
- **[Lec 6](https://docs.google.com/presentation/d/1EYuKHtQM4RIgkvIxrMyAkq02l8KUd9WuCsjCHviBaKI/edit?usp=sharing)**: _Vascular permeability_, compartment modelling, and T1w dynamic contrast-enhanced MRI (DCE-MRI) [Tofts (2018) Ch. [14](https://drive.google.com/open?id=1Wy6ZGurLkV18q6v1XAlhMRfvLttV2f08); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 316-319; Measurement of Renal Perfusion and Filtration with MRI [GitHub](https://github.com/arvidl/functional-kidney-imaging) / [slides](https://docs.google.com/presentation/d/1WS6ODHrXOfYL-fXLw847EkYR4qcvDJA6bRTvqFE_fIY/edit?usp=sharing)]. Video recording from this session: https://youtu.be/X4zGyhid48U
- **[Lec 7](https://docs.google.com/presentation/d/142Y5wQKkIvRkcmBiSV2INDhuMdRHrpPhxqs2zx17ZCY/edit?usp=sharing)**: _Brain connectivity_ assessed with aMRI, dMRI, fMRI and network (graph) theory [Fornito (2016) Ch. [1](https://drive.google.com/open?id=179E3CAZsV6LzV7Jb37eHmczuzVLJUB4H); [Bassett (2018)](https://drive.google.com/open?id=1PW30HroQMBLPLDiZsnhJZ-obumW5RaEA); McRobbie (2017) Ch. [18](https://drive.google.com/open?id=1kAUzG30nGN4a9pPq45jH6pIHPU0EKwyC) pp. 319-325]. Video recording from this session: https://youtu.be/rAbNbpcUNdY
- **Lec 8**: _Outbreak science and COVID-19_ [[README](https://github.com/computational-medicine/BMED360-2021/tree/main/Outbreak-Science-Extra#readme)] (biology, epidemiology, geo-mapping, imaging) [[covid-19-eda](https://nbviewer.jupyter.org/github/computational-medicine/BMED360-2021/blob/main/Outbreak-Science-Extra/epi/covid-19-eda.ipynb)] [[simulitis-outbreak](https://nbviewer.jupyter.org/github/computational-medicine/BMED360-2021/blob/main/Outbreak-Science-Extra/epi/simulitis-outbreak.ipynb)]
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