= Automatic analysis (aa) =
Automatic analysis (aa) is a pipeline system for neuroimaging, written  in Matlab. It supports SPM 5/8 and some functions from FSL.

For more information see:

 * Version 2.2 and earlier: [[AutomaticAnalysisIntroduction|Manual]]
 * Version 4:
  . [[AA|This page]]
  . [[https://github.com/rhodricusack/automaticanalysis|GitHub]]
  . [[https://github.com/rhodricusack/automaticanalysis/wiki|Wiki]]

Any problems, report them to [[DannyMitchell|Danny Mitchell]] (version 2 and 3) or [[TiborAuer|Tibor Auer]] (version 4).

<<TableOfContents(2)>>

== Paths to aa ==
Different versions live in:

 * old versions (0.1beta - 2.0) - {X} unsupported
  . `/imaging/local/spm/aa/aa-ver0.1_beta`
  . `/imaging/local/spm/aa/aa-ver0.2_beta`
  . `...`

 * new versions (2.2 - 4.beta)
  . `/imaging/local/spm/aa_svn_new/versions/release-2.2`
  . `/imaging/local/spm/aa_svn_new/versions/release-3.0`
  . `...`

 * version 4.0 (based on the latest devel-rhodri branch from !GitHub + extended) - {OK} '''recommended'''
  . `/imaging/local/software/AA/release-4.0`

== Using aa ==
=== Configuration ===
Before running aa you need to add the corresponding path to MATLAB Path:

 * File/Set Path...
 * {{{#!highlight matlab numbers=off
addpath('path_to_aa');
savepath;
}}}

(!) To avoid version conflicts make sure that it is added to the '''top''' of the Path.

=== Running ===
Then, you need a [[attachment:aa_simple.m|User Master Script (UMS)|&do=get]]

=== Advanced Features ===
==== Input file ====
It is possible to specify Subjects, Sessions and Events based on a text file.  Required options in aap.acq_details.input (see also aap_parameters_defaults.xml):

 * list: text file:
  . Required format:
   * a CSV file: cells are separated with semicolon
   * subcells are separated with "_"
   * a header in the first line
  . Required columns (may contain more):
   * "ID": numbers for identifying subjects
   * "FMRI1": cells for the fMRI measurement; it must contain the same number of subcells as the coresponding column header
    * first subcell is the CBU volunteer number (without "CBU")
    * series numbers are defined in the consecutive subcells with the same order as their names in the coresponding column header
  . E.g.:
   . {{{#!csv
   ID;Age;Sex;FMRI1_Loc_Con_LDeasy_LDhard
   02;29;f;90952_7_6_4_5
}}}
   As "pure" text:
   . ID;Age;Sex;FMRI1_Loc_Con_LDeasy_LDhard
   . 02;29;f;90952_7_6_4_5

 * selected_sessions: subselection of a subset of series:
  . E.g. (based on the example above): [3 4] --> LDeasy and LDhard

 * referencedirectory_tmpl: a template for path to the folder containing Event files (.mat files in SPM-format)
  . Required format:
   * must contain "*" which will be substituted with "ID" (see above)
  . E.g.: '/imaging/ta02/ActionWords/Analysis/E-P

Then you add this line to your UMS:

{{{#!highlight matlab numbers=off
aap = aas_processinput(aap)
}}}
= Recent Updates =
=== 2013/06/26 merge with the latest devel-rhodri branch from GitHub ===
 * release-4.0 is now the latest stable
 .

=== 2013/06/06 new feature ===
 * NIFTI-4D support added. It works only with '''spm8_fil_r5236'''
 . As a default, NIFTI-3D is set. To enable NIFTI-4D, you have to specify it in the UMS:
 . {{{#!highlight matlab numbers=off
aap.options.NIFTI4D = 1; % 4D support; typical value 0
}}}

=== 2013/05/13 new feature ===
 * Garbage collection tested
 * New report summary:
  * Head movement: outlier-detection with boxplot

=== 2013/04/24 CBSU Patch/Extension for Version 4 is available ===
New features:

 * Handling input file as a list of subjects and sessions (see Advanced Features/Input file)
 * Module for first-level thresholding
  * List of significant activation maps
  * Overlays on axial slices (T1 MNI)
  * Rendering results in 3D
 * Multi-level interlinked reporting:
  * Study (reporting second-level)
  * Subjects (each subjects separately)
  * Summaries:
   * Subjects
   * Registration
   * First-level thresholded maps

{{{#!wiki caution
'''Known bugs:'''

Parallel computing is still not working!
}}}
=== 2013/03/03 Version 4 is available ===
[[https://github.com/rhodricusack/automaticanalysis/wiki/New-features-in-version-4|New features in version 4]]