AA - MRC CBU Imaging Wiki

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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).

Paths to aa

Different versions live in:

  • legacy versions (0.1beta - 2.0) - {X} 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 - {OK} 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 (of SPM's paths), so modification to the spm may have effect.

Running

(!) MATLAB: You need MATLAB newer than the default (r2009a). Most functions have been tested on MATLAB r2012b, so it must be safe to use.

Then, you need a

Parallel computing

Usage

  • 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!

Monitoring

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_CBSU.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

2013/10/29 New features!

  • FreeSurfer has been tested

  • Solving backward-compatibility for handling multiple DICOM sources (see Recent Update on 2013/09/06)

Colon-separated-list (CSL) for rawdatadir:

The “old” script should work without any changes but the newest ones (based on Recent Update on 2013/09/06) should revert. When multiple sources are defined, use CSL. E.g.:

which is default at the moment (see aap_parameters_defaults_CBSU.xml). }}}

2013/09/06 New features!

  • DATREL has been tested

  • Improved monitoring of the parallel computing

  • Handling multiple DICOM sources (e.g. /mridata/cbu and /mridata/camcan)

Known issue (backward compatibility) SOLVED (see above):

If you want to customize DICOM sources, you need to put your own path to source not into rawdatadir directly (as used to), but into rawdatadir.paths (cell array) or rawdatadir.paths{1} (cellstring).

2013/08/08 Parallel computing is working

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
  • NIFTI-4D support is independent from SPM version. N.B.: Configuration!

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.
  • 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