A list of links and resources for my Methods in Neuroimaging Course (PSY 6930).
- Principles of FMRI Lecture series Tor Wager's incomparable lecture series. Deeper into Physics / stats than we'll get.
- fMRI 4 Newbies. Jody Culham's master class. I've borrowed heavily from this! If you need more, start here! If you want even more, check out her links.
- Full Free course from UCL - just sign up with an account If you have the time, this course is everything we'll cover in full form!
- Jeanie Mumford's tutorials mostly on analyses.
- Enigma-U: Youtube tutorials of, well, everything!
- Nancy Kanwisher the Human Brain course
- MRI and physics overview. Nitty gritty physics details.
- MRI Safety. A good overview of safety and procedures.
- MRI Methods collection. From Jonathan Peelle; slightly out of date.
- Collection of summer courses. Great lectures and articles on more advanced topics.
- MVPA Meanderings. Blog on some methodological issues. Some more advanced tutorials.
- Meta-resource on learning fMRI from Jonathan Peelle
- Meta-resource on learning fMRI from Ausaf Farooqui
- Meta-resource on learning fMRI from Chris Rorden See his courses in particular!
- Allen Brain Map anatomy lessons and visualizations.
- Anatomy text Check UF library for e-book and PDF access.
- FMRI Text 1, Huettel et al. The authorative text
- FMRI Text 2, Poldrack et al. Shorter and more focused on analysis
- NeuroStars open forum for questions about analyses, software, debugging, etc.
- Paper summary of MVPA
- Twitter thread with code-focused links. MRI/fMRI focused, mostly based on computational tools.
- Computer science overview. Broad computational toolkit.
- Text on data science for neuroimaging. Computational skills, with a focus on neuroimaging. Also available as an in-print book.
- Text on mathematical tools. More focus on the mathematical background of analyses.
- Advanced methods tutorials from Mark Thornton
- NITRC-Computing Environment
- Andy's Brain book. One stop shop to learn hands-on fMRI preprocessing and analyses. A great starting point!
- Andy's Brain blog. More advanced questions/tutorials.
- NeuroMatch The incomparable!
- For example, see a re-analysis of Mick Bonner's data
- University of Cambridge wiki & meta-resource
- In particular, check here for datasets!
- Brainiak tutorials. Princeton Neuroscience trainings. Very hands on, mostly in Python.
- Brainiak recommended learning computationally focused.
- Human Connectome Project. For human connectome project specific stuff.
- Jared Tanner (UF's own!) analysis pipeline.
- BIDS format info on the neuroimaging data storage standard.
- A list of BIDS converters. Tools and options to try for BIDS conversion.
- Brainlife. All online analyses!
- Neurodesk. Containerized analysis tools - huge range of software available!
- NeuroQuery meta-analysis and lit search tool.
- NeuroSynth (outdated) meta-analysis and lit search tool.
- NeuroSynth Compose more up to date meta-analysis tool.
- And tutorials!
- NiMare Python-based meta-analysis.
- Nipype. Python-based analysis tools (can use FSL, SPM, freesurfer, and more)
- FSL tutorials and guides.
- SPM. Matlab-based analysis tools.
- AFNI. AFNI instructions
- ITKSnap
- NITRC. Datasets and computational tools
- VisualQC. Quality control tools
- PySurfer Python-based visualizations from Gallant lab.
- GLMSingle Extracting single trial betas for
- Tools for visualizations 1 slightly outdated.
- Tools for visualization 2
- Tedana for multi-echo processing
- TemplateFlow - standard brain spaces
- XCP-D: Analysis post-processing pipeline from Penn and others
- Open Neuro approximately 1000 imaging datasets (including EEG, MEG, PET, etc.).
- Neurovault processed brain images.
- Natural Scenes Dataset
- fMRI pre-registration template
- NITRC Dataset resources
- Martinos center: Intro lecture
- MRIllustrated: More in depth physics lecture
- Website intro resource, diffusion-imaging.com
- PyMVPA Python-based multivoxel pattern analysis tools (now a BIDS app!)
- Neuromatch datasets
- Dartbrains tutorial
- Brainiak tutorial