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
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 (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
Features
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
Handling multiple DICOM sources
- 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.:
aap.directory_conventions.rawdatadir = ‘/mridata/cbu:/mridata/csl:/mridata/camcan’; % default at the moment (see aap_parameters_defaults_CBSU.xml)
Support for NIFTI-4D images
- 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
Non-Standard Modules
- 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
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.:
- 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 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
- Required format:
- 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.:
aap.directory_conventions.rawdatadir = ‘/mridata/cbu:/mridata/csl:/mridata/camcan’; % 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 Recent Update on 2013/10/29):
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
See Parallel computing 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
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.
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
Module for first-level thresholding
Multi-level interlinked reporting:
Known bugs:
Parallel computing is still not working!