Useful links and resources

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About

This page was created in an effort to provide a collaborative resource for beginning students in neuroimaging at KI and as a repository for a variety of helpful links. Feel free to add to it!


(f)MRI analysis links

Principles of fMRI - video-based course on Coursera

The UCLA/Semel Neuroimaging Advanced fMRI Summer Program with slides and videos from previous offerings

Andy's Brain Blog and associated Youtube Channel with a ton of hands-on videos on processing imaging data in SPM, FSL and AFNI as well as general tips on statistics, working with Unix-based systems and the programming language R, and many more...

SPM homepage including the SPM course videos and example datasets from the manual with step-by-step analysis instructions

Methods for dummies at UCL

fMRI data analysis videos by Jeanette Mumford

Imaging (and other) wikis of the Cognition and Brain Sciences Unit in Cambridge

Imaging Knowledge Base at MIT

Principles of setting up a script for batch processing in SPM8 (can easily be adapted for newer SPM versions)

OHBM conference videos and slides

Online sample size calculation for fMRI based on pilot data


(f)MRI analysis books

Huettel, S. A., Song, A. W. & McCarthy, G. (2008). Functional magnetic resonance imaging. Sinauer Associates.

Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). Handbook of functional MRI data analysis. Cambridge University Press. Accompanying webpage

Ashby, F. G. (2011). Statistical analysis of fMRI data. MIT press.


Some of these are available around the office for borrowing, just ask around.


(f)MRI datasets

Human Connectome Project with course from 2015

OpenfMRI - Platform to share fMRI datasets

NeuroVault - Unthresholded statistical maps from fMRI experiments

Neurosynth provides automatic aggregation of fMRI activations from several thousand studies


Statistics

using R

RStudio - user-friendly interface for interacting with R

Introduction to R for people with no programming experience (Register to save progress across chapters)

Cookbook for R - Generally good resource for learning R, but particularly useful for plotting nice graphs with the help of ggplot2.

Nice tutorials on linear models and mixed models

statcheck - an R package to check articles (including your own) for correct reporting of statistics

Field, A., Miles, J., & Field, Z. (2012). Discovering Statistics Using R. Sage.

using SPSS

Field, A. (2013). Discovering statistics using IBM SPSS statistics. Sage.


Matlab

Matlab for Psychologists

ICN Matlab for Cognitive Neuroscience Course

Programming experiments with Matlab using the Psychophysics Toolbox


Computational modeling

Introduction to Reinforcement Learning with accompanying Matlab code

Lecture videos from the Computational Psychiatry Course in Zurich 2015


Neurobs Presentation

Programming Tasks for Psychological Experiments using Presentation


Using Git

Git for Humans


Other links

Learning Markdown

Personal tools
MEG