Example Scripts

A number of example scripts are provided in the aa distribution that illustrate a range of aa usage, from basic functionality to more specialized techniques. These can be found under the "examples" directory. The following is a brief description of the current contents.

Note the notation foo.m/xml used here indicates two files: a userscript (foo.m) and a tasklist (foo.xml).

Subdirectory: tutorials

SPM_CH30.m/xml			- SPM auditory task used in the aa tutorial

Subdirectory: demos

These scripts use publically-available data and demonstrate basic aa functionality.

basic.m/xml			- a one-subject standard fMRI analysis
branching1.m/xml		- demonstration of a branched pipeline
branching2.m/xml		- demonstration of multi-level branching
denoising.m/xml			- frame censoring, wavelet despking, ICA, and rWLS
ds000114.m/xml			- a complete analysis of the ds000114 OpenNeuro dataset
ds000114_motor.m/xml		- analysis of the ds000114 motor task only
meeg.m/xml			- EEG analysis of the LEMON dataset.

Subdirectory: cbu

These scripts were developed at the MRC Cognition and Brain Sciences unit at Cambridge. They require access to data at the CBU, but are included in the collection as examples of specialized and more advanced aa applications.

ASL.m/xml			- arterial spin labeling
MTI.m/xml			- magnetisation transfer imaging
diffusion.m/xml			- diffusion kurtosis imaging
diffusion_with_topup.m/xml	- DKI with FSL topup distortion correction
fmri.m/xml			- basic fMRI preprocessing and modeling
fmri_advanced.m/xml		- fMRI processing including DARTEL and surface projection
fmri_connect.m/xml		- demonstration of a "connected" pipeline
fmri_multi.m/xml		- processing of a longitudinal dataset
freesurfer.m/xml		- an aa implementation of Freesurfer's "recon all"
meg.m/xml			- a basic MEG pipeline
structural.m/xml		- structural processing used in fmri_connect