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: Manual

• Version 4:

  • This page

  • GitHub

  • Wiki

Any problems, report them to Danny Mitchell (version 2 and 3) or Tibor Auer (version 4).

Paths to aa

Different versions live in:

• legacy versions (0.1beta - 2.0) - unsupported

  • /imaging/local/spm/aa/aa-ver0.1_beta

  • /imaging/local/spm/aa/aa-ver0.2_beta

  • ...

• old 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

  • ...

• new version (4.0 - 4.1) (based on the latest devel-share branch from GitHub)

  • /imaging/local/software/AA/release-4.0

  • /imaging/local/software/AA/release-4.1 - recommended

Using aa

Configuration

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

• File/Set Path...

• addpath('path_to_aa');
  aa_ver4_nocloud; % adds aa subfolders to the path
  savepath;
  

To avoid version conflicts make sure that it is added to the top of the Path. It is even more important that path_to_aa/extrafunctions/spm_mods is on the top, so modification to the spm may have effect.

Running

Then, you need a User Master Script (UMS)

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.:

    • 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 withID (see above)

    • E.g.: '/imaging/ta02/ActionWords/Analysis/E-Prime/DAW*/ref'

  • The folder should contain the regressor(s) in SPM format (.mat file) with filename format: condition_vol_ID-Session Name.mat.

    • E.g. (based on the example above): condition_vol_2-LDeasy.mat
• Then you add these lines to your UMS (based on the example above):

• aap.acq_details.input.list='/imaging/ta02/ActionWords/Analysis/Subject_List_Test.csv';
  aap.acq_details.input.selected_sessions = [3 4];
  aap.acq_details.input.referencedirectory_tmpl = '/imaging/ta02/ActionWords/Analysis/E-Prime/DAW*/ref';
  aap = aas_processinput(aap);
  

Recent Updates

2013/08/08 Parallel computing is working

• To enable parallel computing you have to be logged in an appropriate computing machine (login11-14) and add the following line to your UMS:

• aap.options.wheretoprocess = 'qsub'; % parallel; typical localsingle
  

• Because each thread will load the saved MATLAB path, it is very important that it is set and saved correctly before initiating parallel jobs. See Configuration for more information!

• Known bugs:

  Conventional SPM diagnostic will be missing for:

  • aamod_realignunwarp (only fieldmaps)
  • aamod_coreg_noss

  However, FSL diagnostics are unaffected.

2013/08/02 new version v4.1 (latest devel-share branch from GitHub)

• merge with GitHub completed

• release-4.1 is now the latest stable

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:

• 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

2013/03/03 Version 4 is available

New features in version 4