Installing CANlab Core Tools

Contents

About the CANlab Core Tools repository and CANlab toolboxes

The CANlab Core Tools repository is on https://github.com/canlab/CanlabCore It contains core tools for MRI/fMRI/PET analysis from the Cognitive and Affective Neuorscience Lab (Tor Wager, PI) and our collaborators. Many of these functions are needed to run other toolboxes, e.g., the CAN lab?s multilevel mediation and Martin Lindquist?s hemodynamic response estimation toolboxes.

The tools include object-oriented tools for doing neuroimaging analysis with simple commands and scripts that provide high-level functionality for neuroimaging analysis. For example, there is an "fmri_data" object type that contains neuroimaging datasets (both PET and fMRI data are ok, despite the name). If you have created and object called my_fmri_data_obj, then plot(my_fmri_data_obj) will generate a series of plots specific to neuroimaging data, including an interactive brain viewer (courtesy of SPM software). predict(my_fmri_data_obj) will perform cross-validated multivariate prediction of outcomes based on brain data. ica(my_fmri_data_obj) will perform independent components analysis on the data, and so forth.

There are a wide range of functions and techniques that we've used in the CANlab. Most of these are supported by specific functionality in our object-oriented tools. You can download other toolboxes from: https://github.com/canlab

And you can find an overview of core object-oriented tool functionality and demos/walkthroughs on https://canlab.github.io

CANlab Toolboxes

Tutorials, overview, and help: https://canlab.github.io

Toolboxes and image repositories on github: https://github.com/canlab

CANlab Core Tools	https://github.com/canlab/CanlabCore
CANlab Neuroimaging_Pattern_Masks repository	https://github.com/canlab/Neuroimaging_Pattern_Masks
CANlab_help_examples	https://github.com/canlab/CANlab_help_examples
M3 Multilevel mediation toolbox	https://github.com/canlab/MediationToolbox
M3 CANlab robust regression toolbox	https://github.com/canlab/RobustToolbox
M3 MKDA coordinate-based meta-analysis toolbox	https://github.com/canlab/Canlab_MKDA_MetaAnalysis

Here are some other useful CANlab-associated resources:

Paradigms_Public - CANlab experimental paradigms	https://github.com/canlab/Paradigms_Public
FMRI_simulations - brain movies, effect size/power	https://github.com/canlab/FMRI_simulations
CANlab_data_public - Published datasets	https://github.com/canlab/CANlab_data_public
M3 Neurosynth: Tal Yarkoni	https://github.com/neurosynth/neurosynth
M3 DCC - Martin Lindquist's dynamic correlation tbx	https://github.com/canlab/Lindquist_Dynamic_Correlation
M3 CanlabScripts - in-lab Matlab/python/bash	https://github.com/canlab/CanlabScripts

Object-oriented, interactive approach The core basis for interacting with CANlab tools is through object-oriented framework. A simple set of neuroimaging data-specific objects (or classes) allows you to perform interactive analysis using simple commands (called methods) that operate on objects.

Map of core object classes:

Dependencies

For full functionality, the other toolboxes below are recommended:

Installing SPM

! Important: You will also need to install spm12 separately, and add it to your matlab path. The latest version at the time of writing is SPM12, which can be downloaded here:

https://www.fil.ion.ucl.ac.uk/spm/software/spm12/

Quick start instructions

Repeat the Clone/genpath/addpath steps for the Neuroimaging_Pattern_Masks repository, and save the path again.

Quick start: Batch install script

The main goal of the code below is to run: canlab_toolbox_setup This is a script that attempts to: # Check for CANlab repositories on your computer # Download any that are missing # Add them to your Matlab path with subfolders.

Note: Unfortunately as of Jan 2020 this does not work well on everyone's computers, due to OS-related variability. The workaround is to install them manually as per the instructions above.

canlab_toolbox_setup is in the CanlabCore repository. So before you run it the CANlab_Core_Tools must be added to your path with subfolders. Otherwise, you will get errors.

The script canlab_toolbox_setup can help download and install the toolboxes you need.

First, go to a folder where you want to install toolboxes/repositories on your hard drive. Mine are in "Github" and I've already installed CanlabCore, so let's find it and go there:

% Locate the CanlabCore Github files on your local computer:
% ------------------------------------------------------------------------

mypath = what(fullfile('CanlabCore', 'CanlabCore'));

% Check if we've got it
if isempty(mypath)
    disp('Download CanlabCore from Github, and go to that folder in Matlab')
    disp('by dragging and dropping it from Finder or Explorer into the Matlab Command Window')
    return
else
    % Add CanlabCore to Matlab path with subfolders
    g = genpath(mypath(1).path);
    addpath(g);

end

mypath = mypath(1).path;

% Set the folder in which the repositories will be installed
% ------------------------------------------------------------------------

% This is the location (folder) in which the repositories will be installed:
base_dir_for_repositories = fileparts(fileparts(mypath));

cd(base_dir_for_repositories)
fprintf('\nInstalling repositories in %s\n', base_dir_for_repositories);

% Find the setup file, canlab_toolbox_setup.m
% ------------------------------------------------------------------------

% This is the file
setupfile = fullfile(mypath, 'canlab_toolbox_setup.m');

% Make sure we've got it
if ~exist(setupfile, 'file')
    disp('Something went wrong.  I can''t find canlab_toolbox_setup.m');
    disp('This file should be included in the CanlabCore Github repository.')
end

% Run the setup script:
% ------------------------------------------------------------------------
%
% Note: This can be system-dependent and may not work on all computers.
% If it doesn't, you can default to cloning the CANLab repositories and
% adding them with subfolders to your Matlab path. The most important ones
% starting out are CanlabCore and Neuroimaging_Pattern_Masks
% e.g.,
% |git clone https://github.com/canlab/CanlabCore.git|
% |git clone https://github.com/canlab/Neuroimaging_Pattern_Masks.git|

canlab_toolbox_setup

% This will attempt to locate toolboxes, add them to your path, and give
% you the option to download them from Github if it can't find them.

% It looks for and installs toolboxes in the current directory,
% which (thanks to the code above) is the path name in base_dir_for_repositories

Installing repositories in /Users/torwager/Documents/GitHub

-----------------------------------------
Checking and/or installing CANlab tools in:
/Users/torwager/Documents/GitHub
-----------------------------------------
Looking for CANlab repositories and adding to Matlab path:
 
CANlab core tools - Object-oriented interactive analysis and tools used in other functions	CanlabCore
CANlab help examples - Example scripts and html output, second-level analysis batch scripts	CANlab_help_examples
MKDA meta-analysis toolbox - Coordinate-based meta-analysis of neuroimaging data	Canlab_MKDA_MetaAnalysis
FMRI_simulations - Misc tools for simulating and testing power and image data	FMRI_simulations
Private masks and signatures - Selected models shared on request	MasksPrivate
M3 Mediation toolbox - Single and Multi-level mediation tools	MediationToolbox
Neuroimaging_Pattern_Masks - meta-analysis masks, signatures, parcellations	Neuroimaging_Pattern_Masks
Robust regression toolbox - Voxel-wise robust regression for neuroimaging data	RobustToolbox
CanlabPrivate - Private repository for lab members and collaborators	CanlabPrivate

-----------------------------------------

-----------------------------------------

Repository: CANlab core tools - Object-oriented interactive analysis and tools used in other functions
Site:CanlabCore
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/CanlabCore -name "fmri_data.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/CanlabCore

-----------------------------------------

Repository: CANlab help examples - Example scripts and html output, second-level analysis batch scripts
Site:CANlab_help_examples
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/CANlab_help_examples -name "a2_second_level_toolbox_check_dependencies.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/CANlab_help_examples

-----------------------------------------

Repository: MKDA meta-analysis toolbox - Coordinate-based meta-analysis of neuroimaging data
Site:Canlab_MKDA_MetaAnalysis
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/Canlab_MKDA_MetaAnalysis -name "i_density.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/Canlab_MKDA_MetaAnalysis

-----------------------------------------

Repository: FMRI_simulations - Misc tools for simulating and testing power and image data
Site:FMRI_simulations
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/FMRI_simulations -name "power_figure3_num_comparisons.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/FMRI_simulations

-----------------------------------------

Repository: Private masks and signatures - Selected models shared on request
Site:MasksPrivate
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/MasksPrivate -name "apply_nps.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/MasksPrivate

-----------------------------------------

Repository: M3 Mediation toolbox - Single and Multi-level mediation tools
Site:MediationToolbox
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/MediationToolbox -name "mediation_brain.m"
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict. 
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/MediationToolbox

-----------------------------------------

Repository: Neuroimaging_Pattern_Masks - meta-analysis masks, signatures, parcellations
Site:Neuroimaging_Pattern_Masks
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/Neuroimaging_Pattern_Masks -name "apply_all_signatures.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/Neuroimaging_Pattern_Masks

-----------------------------------------

Repository: Robust regression toolbox - Voxel-wise robust regression for neuroimaging data
Site:RobustToolbox
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/RobustToolbox -name "robust_results_batch.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/RobustToolbox

-----------------------------------------

Repository: CanlabPrivate - Private repository for lab members and collaborators
Site:CanlabPrivate
Finding repo: Running command:
find /Users/torwager/Documents/GitHub/CanlabPrivate -name "power_calc.m"
Found and added to path with subfolders: /Users/torwager/Documents/GitHub/CanlabPrivate

-----------------------------------------

All CANlab repositories previously installed. Saving path

Published with MATLAB® R2018a