Uploaded April 2021 | Updated September 2026, 2 weeks ago
Rafael Henriques' workshop on DIPY, recorded 23-24 November, 2020.
Workshop materials and notebooks: github.com/RafaelNH/pybrain_dipy
00:00:00 Introduction: about Rafael and DIPY
00:05:01 How to install DIPY and workshop materials
00:09:01 Why diffusion MRI
00:17:33 Q&A
00:23:29 Tutorial 1: load and explore data
00:36:08 Diffusion tensor imaging
00:42:51 Loading your own data
00:46:57 Q&A
00:48:15 Tutorial 2: DTI
00:55:17 DTI tractography
00:58:25 Q&A
01:03:25 Tutorial 3: DTI deterministic tractography
01:12:29 Probabilistic tractography
01:14:28 Tutorial 4: DTI probabilistic tractography
01:18:54 DIPY simulations: DTI limitations 1
01:24:13 High angular resolution diffusion imaging
01:32:40 Q&A, How to get help with DIPY
01:40:27 Tutorial 5: HARDI deterministic tractography
01:48:28 Tutorial 6: HARDI probabilistic tractography
01:53:19 Using Spyder instead of Jupyter Notebook
01:57:44 Day 2 introduction and day 1 recap
01:58:13 DIPY Simulations: HARDI signals
01:59:56 DIPY Simulations: DTI limitations 2
02:18:38 Q&A
02:24:34 Tutorial 7: diffusion kurtosis imaging
02:35:50 Preprocessing diffusion MRI data
02:49:21 Q&A on Rician noise
02:53:16 Tutorial 8: PCA denoising
03:03:24 Tutorial 9: Gibbs unringing
03:08:56 Diffusion models
03:25:03 Tutorial 10: Extracting SMT2 estimates from MSDKI
03:30:00 White matter tract integrity (WMTI) model
03:32:26 Tutorial 11: Reconstruction with WMTI model
03:37:38 Free water DTI model
03:41:06 Tutorial 12: Free water DTI (FWDTI)
03:46:49 FWDTI implementation in DIPY
03:50:54 Advanced diffusion models
03:53:55 Overview of other DIPY tutorials and tools
04:08:27 Future directions in diffusion MRI
For more on the python for brain imaging (pybrain) workshop series, see pybrain-workshop.github.io
Rafael Henriques' workshop on DIPY, recorded 23-24 November, 2020.
Workshop materials and notebooks: github.com/RafaelNH/pybrain_dipy
00:00:00 Introduction: about Rafael and DIPY
00:05:01 How to install DIPY and workshop materials
00:09:01 Why diffusion MRI
00:17:33 Q&A
00:23:29 Tutorial 1: load and explore data
00:36:08 Diffusion tensor imaging
00:42:51 Loading your own data
00:46:57 Q&A
00:48:15 Tutorial 2: DTI
00:55:17 DTI tractography
00:58:25 Q&A
01:03:25 Tutorial 3: DTI deterministic tractography
01:12:29 Probabilistic tractography
01:14:28 Tutorial 4: DTI probabilistic tractography
01:18:54 DIPY simulations: DTI limitations 1
01:24:13 High angular resolution diffusion imaging
01:32:40 Q&A, How to get help with DIPY
01:40:27 Tutorial 5: HARDI deterministic tractography
01:48:28 Tutorial 6: HARDI probabilistic tractography
01:53:19 Using Spyder instead of Jupyter Notebook
01:57:44 Day 2 introduction and day 1 recap
01:58:13 DIPY Simulations: HARDI signals
01:59:56 DIPY Simulations: DTI limitations 2
02:18:38 Q&A
02:24:34 Tutorial 7: diffusion kurtosis imaging
02:35:50 Preprocessing diffusion MRI data
02:49:21 Q&A on Rician noise
02:53:16 Tutorial 8: PCA denoising
03:03:24 Tutorial 9: Gibbs unringing
03:08:56 Diffusion models
03:25:03 Tutorial 10: Extracting SMT2 estimates from MSDKI
03:30:00 White matter tract integrity (WMTI) model
03:32:26 Tutorial 11: Reconstruction with WMTI model
03:37:38 Free water DTI model
03:41:06 Tutorial 12: Free water DTI (FWDTI)
03:46:49 FWDTI implementation in DIPY
03:50:54 Advanced diffusion models
03:53:55 Overview of other DIPY tutorials and tools
04:08:27 Future directions in diffusion MRI
For more on the python for brain imaging (pybrain) workshop series, see pybrain-workshop.github.io
