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:
old versions (0.1beta - 2.0) -
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) -
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.:
- As "pure" text:
- ID;Age;Sex;FMRI1_Loc_Con_LDeasy_LDhard
- 02;29;f;90952_7_6_4_5
- Required format:
- 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
- Required format:
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!