AA - MRC CBU Imaging Wiki

Revision 75 as of 2013-06-27 13:18:50

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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:

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

Contents

  1. Automatic analysis (aa)
    1. Paths to aa
    2. Using aa
  2. Recent Updates

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... 
  • 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 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 with "ID" (see above)
    • E.g.: '/imaging/ta02/ActionWords/Analysis/E-P

Then you add this line to your UMS: 

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: 
  • 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

Known bugs:

Parallel computing is still not working!

2013/03/03 Version 4 is available

New features in version 4