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| * Version 4: [[https://github.com/rhodricusack/automaticanalysis|GitHub]] [[https://github.com/rhodricusack/automaticanalysis/wiki|Wiki]] |
* Version 4: . [[AA|This page]] . [[https://github.com/rhodricusack/automaticanalysis|GitHub]] . [[https://github.com/rhodricusack/automaticanalysis/wiki|Wiki]] |
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| Any problems, report them to [[DannyMitchell|Danny Mitchell]] or [[TiborAuer|Tibor Auer]]. | Any problems, report them to [[DannyMitchell|Danny Mitchell]] (version 2 and 3) or [[TiborAuer|Tibor Auer]] (version 4). <<TableOfContents(2)>> == 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 - /!\ not debugged . `/imaging/local/spm/aa4_github/automaticanalysis` . `/imaging/local/software/AA/release-4.0` * version 4.0 (debugged and extended) - {OK} '''recommended''' . `/imaging/local/software/AA/release-4.0p` == Using aa == === Configuration === Before running aa you need to add the corresponding path to MATLAB Path: * File/Set Path... * {{{#!highlight matlab numbers=off 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 [[attachment:aa_simple.m|User Master Script|&do=get]] = Recent Updates = === 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 User Master Script: . {{{#!highlight matlab numbers=off 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 (apart from debugging): * Handling input file as a list of subjects and sessions * 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 {{{#!wiki caution '''Known bugs:''' Parallel computing is still not working! }}} === 2013/03/03 Version 4 is available === [[https://github.com/rhodricusack/automaticanalysis/wiki/New-features-in-version-4|New features in version 4]] |
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 -
![/!\](/basewiki/moin_static1910/moniker_cbu/img/alert.png "/!\")
not debugged /imaging/local/spm/aa4_github/automaticanalysis
/imaging/local/software/AA/release-4.0
version 4.0 (debugged and extended) -
recommended /imaging/local/software/AA/release-4.0p
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
Recent Updates
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 User Master Script:
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 (apart from debugging):
- Handling input file as a list of subjects and sessions
- 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!