This resource is sponsored by the University of Michigan.
Hello! This book, Andy's Brain Book, is the ReadTheDocs companion to Andy's Brain Blog. It is intended for fMRI beginners, with more advanced imaging techniques being added later on. If this is your first time here, watch this video for a quick overview of the website.
This book, Andy's Brain Book, is intended for fMRI beginners, with more advanced imaging techniques being added later on.
If you are completely new to fMRI analysis, I recommend starting with the :ref:`installation page <fsl_mac_install>`. Good luck!
Note
Reading this book is easier with a slightly larger font size; I recommend using a zoom of 125%. You can do this on a Macintosh by holding down the Command key and pressing +, or from the browser menu you can click on View -> Zoom In.
.. toctree:: :maxdepth: 1 :caption: Install installation/fsl_mac_install
.. toctree::
:maxdepth: 1
:caption: Unix for Neuroimagers
unix/Unix_Intro
unix/Unix_01_Navigation
unix/Unix_02_CopyRemove
unix/Unix_03_ReadingTextFiles
unix/Unix_04_ShellsVariables
unix/Unix_05_ForLoops
unix/Unix_06_IfElse
unix/Unix_07_Scripting
unix/Unix_08_Sed
unix/Unix_09_AutomatingTheAnalysis
.. toctree::
:maxdepth: 1
:caption: fMRI Short Course with FSL
fMRI_Short_Course/fMRI_Intro
fMRI_Short_Course/fMRI_01_DataDownload
fMRI_Short_Course/fMRI_02_ExperimentalDesign
fMRI_Short_Course/fMRI_03_LookingAtTheData
fMRI_Short_Course/fMRI_04_Preprocessing
fMRI_Short_Course/fMRI_05_1stLevelAnalysis
fMRI_Short_Course/fMRI_06_Scripting
fMRI_Short_Course/fMRI_07_2ndLevelAnalysis
fMRI_Short_Course/fMRI_08_3rdLevelAnalysis
fMRI_Short_Course/fMRI_09_ROIAnalysis
fMRI_Short_Course/fMRI_10_Summary
fMRI_Short_Course/fMRI_Appendices
.. toctree::
:maxdepth: 1
:caption: FreeSurfer
FreeSurfer/FreeSurfer_Introduction
.. toctree::
:maxdepth: 1
:caption: E-Prime
E-Prime/E-Prime_Overview
.. toctree::
:maxdepth: 1
:caption: AFNI
AFNI/AFNI_Overview
.. toctree::
:maxdepth: 1
:caption: SPM
SPM/SPM_Overview
.. toctree::
:maxdepth: 1
:caption: Functional Connectivity with the CONN Toolbox
FunctionalConnectivity/CONN_Overview
.. toctree::
:maxdepth: 1
:caption: Parametric Modulation
PM/PM_Overview
Note
The following modules are under construction. Check back soon for more updates!
.. toctree:: :maxdepth: 1 :caption: Image Visualization with MRIcroGL MRIcroGL/MRIcroGL_Overview
.. toctree:: :maxdepth: 1 :caption: Introduction to the Human Connectome Project (HCP) HCP/HCP_Overview
.. toctree:: :maxdepth: 1 :caption: Finite Impulse Response (FIR) Models FIR/FIR_Overview
.. toctree:: :maxdepth: 1 :caption: fMRI Concepts Practicals/DesignOptimization
.. toctree::
:maxdepth: 1
:caption: Diffusion Analysis with MRtrix
MRtrix/MRtrix_Introduction
.. toctree::
:maxdepth: 1
:caption: ASL Analysis
ASL/ASL
ASL/ASL_Techniques
ASL/fASL_02_Download
ASL/fASL_03_Task
ASL/04_fASL_GUI
ASL/05_fASL_Results
ASL/06_fASL_Quantification
.. toctree::
:maxdepth: 1
:caption: Frequently Asked Questions
FrequentlyAskedQuestions/FrequentlyAskedQuestions.rst
.. toctree::
:maxdepth: 1
:caption: Statistics
Statistics/GIMME
.. toctree::
:maxdepth: 1
:caption: Miscellaneous
Miscellaneous/ConvertingDICOMs
.. toctree::
:maxdepth: 1
:caption: Open Science
OpenScience/OS_Overview
.. toctree::
:maxdepth: 1
:caption: Advanced Normalization Tools (ANTs)
ANTs/ANTs_Overview
.. toctree::
:maxdepth: 1
:caption: Tract-Based Spatial Statistics (TBSS)
TBSS/TBSS_Overview
.. toctree::
:maxdepth: 1
:caption: Statistics for Neuroimagers
Stats/Stats_Overview
.. toctree::
:maxdepth: 1
:caption: Machine Learning for Neuroimagers
ML/ML_Overview
.. toctree::
:maxdepth: 1
:caption: Slicer
Slicer/Slicer_Overview
.. toctree::
:maxdepth: 1
:caption: CAT12
CAT12/CAT12_Overview
.. toctree::
:maxdepth: 1
:caption: Using the Supercomputer
Supercomputer/Supercomputer_Overview
.. toctree::
:maxdepth: 1
:caption: Matlab for Neuroimagers
Matlab/Matlab_Overview
.. toctree::
:maxdepth: 1
:caption: ITK-Snap
ITK-Snap/ITK-Snap_Overview
.. toctree::
:maxdepth: 1
:caption: Python for Neuroimagers
PythonForNeuroimagers/PythonForNeuroimagers_Overview
.. toctree::
:maxdepth: 1
:caption: Meta-Analysis for fMRI
MetaAnalysis/MetaAnalysis_Overview
Note
This book is under construction. More chapters will be added in the coming weeks; my goal is to have a complete draft of the fMRI Short Course by the first week of June.
4.24.2019: Finished the sections Unix Tutorial #4, fMRI Short Course chapters on smoothing and quality checking FEAT output, and added a playlist covering all of the sections done in the Preprocessing module.
5.06.2019: Added sections to FAQ about resampling, biased analyses, and flipped orientations. Wrote the chapters for the Statistics part of the short course; videos coming soon.
5.25.2019: Finished the Unix Module, and added videos for 2nd and 3rd level analysis in the fMRI short course.
5.31.2019: First draft of the Unix and fMRI courses are complete.
10.14.2019: E-Prime module is complete.
10.16.2019: FreeSurfer module complete.
1.13.2020: SPM written module complete (videos not up yet)
4.13.2020: SPM videos uploaded
5.21.2020: CONN Tutorials complete
12.08.2020: First part of MVPA tutorial complete, from preprocessing to group-level analysis. Later on, will add other statistical analyses, such as prevalence analysis.
01.20.2022: There is now a DOI for Andy's Brain Book! If you would like to cite it, use the following template: "We followed the AFNI preprocessing pipeline as outlined in Andy's Brain Book (Jahn, 2022. doi:10.5281/zenodo.5879293)."