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Coding in Python
Alexander Holmes edited this page Jul 5, 2023
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This course covers the basics of programming within Python through the lens of neuroscience and neuroimaging.
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It covers basics from variables and loops, to data manipulation and statistics.
- Most other plotting tools (including ones listed below) are built upon Matplotlib, so these are important fundamentals
edX ~1 hour
- This will give you a very brief introduction to Python and programming, including an introduction to variables and if statements
DataCamp ~4 hours
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This course is slightly longer but addresses many topics in more detail.
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The material is taught with an emphasis on data science, which may be useful for broader industry careers and avenues outside of academia (although it's still helpful for academia too)
France Universite Numerique (FUN) ~20-30 hours
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Semi-introductory course to Python with an emphasis on machine learning.
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For new PhD students, this can be claimed for your graduate PD hours by submitting the corresponding form on the HDR website
Basic guide that covers types of variables, lists, dicts, functions, numpy, matplotlib, etc.
- 0.0 Home
- 0.1 Neuroscience fundamentals
- 0.2 Reproducible Science
- 0.3 MRI Physics, BIDS, DICOM, and data formats
- 0.4 Introduction to Diffusion MRI
- 0.5 Introduction to Functional MRI
- 0.6 Measuring functional and effective connectivity
- 0.7 Connectomics, graph theory, and complexity
- 0.8 Statistical and Mathematical Tidbits
- 0.9 Introduction to Psychopathology
- 0.10 Introduction to Genetics and Bioinformatics
- 0.11 Introduction to Programming
- 1.0 Working on the Cluster
- 2.0 Programming Languages
- 2.1 Python
- 2.2 MATLAB
- 2.3 R and RStudio
- 2.4 Programming Intro Exercises
- 2.5 git and GitHub
- 2.6 SLURM and Job Submission
- 3.0 Neuroimaging Tools and Packages
- 3.1 BIDS
- 3.2 FreeSurfer
- 3.2.1 Qdec
- 3.3 FSL
- 3.3.1 ICA-FIX
- 3.4 Connectome Workbench/wb_command
- 3.5 fMRIPrep
- 3.6 QSIPrep
- 3.7 HCP Pipeline
- 3.8 tedana
- 4.0 Quality control
- 4.1 MRIQC
- 4.2 Common Artefacts
- 4.3 T1w
- 4.4 rs-fMRI
- 5.0 Specialist Tools
- 6.0 Putting it all together