00 fMRI Resource

Textbook¶

Basic Reading¶

• Principles of fMRI by Tor D. Wager and Martin A. Lindquist

  • Great introduction for newbies to get started within only 200 pages.

• Handbook of Functional MRI Data Analysis by Russell A. Poldrack

  • Brief introduction of fMRI data analysis, not a hands-on manual. The cons is that it was published in 2011

• Functional Magnetic Resonance Imaging by Scott A. Huettel, Allen W. Song, and Gregory McCarthy

  • Highly Recommend Classic textbook on fMRI, very comprehensive. The first few chapters can be skipped if you find them difficult to understand (e.g. the formula section)

Advanced Reading¶

• Ombao, H., Lindquist, M., Thompson, W., & Aston, J. (Eds.). (2016). Handbook of Neuroimaging Data Analysis (1st ed.). Chapman and Hall/CRC. Chapman,Hall/CRC (2016)

• Introduction to Neuroimaging Analysis by Mark Jenkinson and Michael Chappell

  • Overly detailed introduction to neuroimaging statistical analysis. But recommended reading

• Statistical Analysis of fMRI Data By F. Gregory Ashby

  • Required strong math foundation

fMRI principles¶

Video¶

Good for newbies

• Fundamental Neuroscience for Neuroimaging, Coursera

  • A very basic introduction to neuroscience and neuroimaging course.

• The following two online courses are particularly focused on fMRI, I highly recommend studying it in conjunction with the textbook of the same name. In fact, previewing the textbook before watching the video will help you learn it. The second half of the course will become challenging due to the data analysis and statistical content (in fact I think this part is taught too fast). If you find it difficult to learn, I suggest you take a break from the course and read the book Functional Magnetic Resonance Imaging.

  • coursera Principles of fMRI 1

  • coursera Principles of fMRI 2

  • https://www.youtube.com/@principlesoffmri6920

Systematic Training

• University of Michigan | Training Course in fMRI

  • Summer class, renew every year. Very systematic.

• Research Methods in Cognitive Neuroscience - 2018-19

  • This video series introduces different research methods in brain science in an easy-to-understand way. The Python video series is great as well.

• MIT fMRI Bootcamp

• https://www.youtube.com/playlist?list=PLjBt5Iq93BT9eXMsgevVTXKVv4BgVLB1X

• https://sites.google.com/berkeley.edu/ee225-sp21

• https://www.coursera.org/learn/mri-fundamentals

• https://www.youtube.com/playlist?app=desktop&list=PL20gKJcYxxBU3kXvu58vf-lL2XxtLHtRL

• https://www.youtube.com/playlist?list=PLA3v5BKsMh2UIXgnt_8QO32ysRERU9hfV

Website¶

• https://cbmm.mit.edu/learning-hub

  • MIT produces a website that regularly puts up neuroscience lectures. They also have YouTube channel.

  • https://www.youtube.com/@MITCBMM/featured

• https://sites.dartmouth.edu/canlab/training-courses/

  • List resources that might be useful.

• https://www.fmri4newbies.com/

  • List some lecture slides.

• http://jonathanpeelle.net/learning-mri

  • Recommended reading, it provides direction for your study.

• https://mindsummerschool.org/

  • shared some course materials, including lectures.

• https://cosanlab.com/resources

• https://fmrif.nimh.nih.gov/index.php/SummerCourse#2024

  • A list of resource.

fMRI Data Analysis¶

• https://www.med.unc.edu/psych/research/niral/download/download-documents

Video¶

AFNI Hands-on

• https://youtube.com/playlist?list=PL_CD549H9kgq-_HSwvH5KhFl8A15u6d71&si=g0mYDdvX0VhdVvGn

• https://www.youtube.com/playlist?list=PLIQIswOrUH699VfdagYNK6zaAHt5tAZcv

Python

• https://youtube.com/playlist?list=PLIQIswOrUH6_szyxn9Fy-2cxd3vjlklde&si=au43tMOaSeG0U2my

• https://www.youtube.com/playlist?list=PLtfEWMIgWS22MMZjPIzBRE2cHhMcvEKwp

• https://www.youtube.com/watch?v=gMuxB18Cr0o

• https://www.youtube.com/watch?v=4FVGn8vodkc&t=1s

• https://www.youtube.com/playlist?list=PLIQIswOrUH6_szyxn9Fy-2cxd3vjlklde

Website¶

AFNI

• https://afni.nimh.nih.gov/

  • The best material to learn, but difficult to start with.

• https://andysbrainbook.readthedocs.io/en/latest/

  • Best introduction for AFNI.

• https://psychiatry.ucsd.edu/research/programs-centers/snl/resources/scanning-meeting/afni-class-01.html

  • some AFNI notes

• https://afni.nimh.nih.gov/pub/dist/edu/latest/

• https://brainhack-princeton.github.io/handbook/index.html

• https://cloud.wikis.utexas.edu/wiki/spaces/~mvf327/pages/70002180/fMRI+Training+Tutorials

• https://www.brown.edu/carney/mri/researchers/analysis-pipelines

  • Provide code for analysis of Resting State fMRI (RS-fMRI), Diffusion Tensor Imaging (DTI), and Multi-Voxel Pattern Analysis (MVPA).

• https://dartbrains.org/content/2019_Spring.html

  • Based on Python. More challenging because the creator has a computational neuroscience background, but you can skip the formulas. I recommend checking out his GitHub page as he shares a lot of resources.

• https://web.stanford.edu/group/spanlab/cgi-bin/wiki/index.php?title=Lab_Manual:FMRI_Data_Analysis

  • A website with very complete information.

Python

• https://neuroimaging-data-science.org/root.html

• https://lukas-snoek.com/NI-edu/index.html

• https://github.com/dartmouth-pbs/psyc161

• https://github.com/ContextLab/cs-for-psych

• Tutorial_Resources.md

  • A list of tutorials and other resources useful for open science and neuroimaging

• https://neuraldatascience.io/intro.html#downloading-the-materials-to-work-through-the-book

• https://github.com/carpentries-incubator/SDC-BIDS-sMRI

• https://dartbrains.org/content/Intro_to_Neuroimaging.html

• https://brainiak.org/tutorials/02-data-handling/

• https://github.com/fMRIAnalysisCourse/fmri-analysis-course

Other¶

• https://miykael.github.io/nipype_tutorial/

• https://osf.io/w2y7q/wiki/home/

• https://docs.ccv.brown.edu/bnc-user-manual

  • https://sites.brown.edu/cnrc-core/resources-and-help/

Brain Function and Anatomy¶

Textbook¶

• Nolte’s The Human Brain An Introduction to its Functional Anatomy by Todd W. Vanderah, Douglas J. Gould

• Atlas of Regional Anatomy of the Brain Using MRI With Functional Correlations by Jean C. Tamraz , Youssef G. Comair

Video¶

• https://www.neuroanatomy.ca/index.html

  • UBC neuroanatomy

• https://www.youtube.com/@mikexcohen1/playlists

  • Great youtube channel with introduction to the principles of brain imaging.

Website¶

• https://www.learnmedicalneuroscience.nl/

• https://www.brainfacts.org/3d-brain#intri=true&focus=Brain

• https://www.brainvoyager.com/webapps/braintutor/BrainTutor.html

• http://www.g2conline.org/3dbrain/

• https://neurosynth.org/

  • a meta analysis of brain region functions

• https://rcweb.dartmouth.edu/CANlab/brainstemwiki/doku.html

  • Brainstem anatomy WIKI

• https://sites.google.com/dartmouth.edu/canlab-brainpatterns/home

• https://web.conn-toolbox.org/

  • functional connectivity toolbox