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At the MRC CBU, aa is already installed centrally and you should not need this page.

Licence Agreement

Automated Analysis software was developed by Dr Rhodri Cusack for supporting research at the MRC Cognition and Brain Science Unit. It is made available to the academic community in the hope that it may prove useful.

Definitions

AA means the Automated Analysis software package and any associated documentation whether electronic or printed. USER means any person or organisation that uses AA. ACADEMIC means not-for-profit.

By using AA, the USER hereby agrees to the following conditions:

Grant

AA is copyrighted by MRC and protected by European Copyright Law. All rights are reserved worldwide.

MRC grants USER the royalty free right under MRC Copyright and MRC intellectual property rights to use AA for ACADEMIC purposes only. If USER wishes to use AA for commercial for-profit purposes then USER will contact MRC for a commercial licence.

Contact details

Rhodri Cusack MRC Cognition and Brain Sciences Unit, 15 Chaucer Road, Cambridge, CB2 2EF Tel: +44 (0) 1223 273 689 Fax: +44 (0) 1223 359 062 Rhodri.Cusack [at] mrc-cbu.cam.ac.uk

Duncan Young Business Manager Medical Research Council Technology 20 Park Crescent London W1B 1AL Tel: +44 (0)207 291 5329 Fax: +44 (0)207 291 5325 duncan.young [at] tech.mrc.ac.uk

The USER will not pass the AA to any other party unless it is accompanied by this Licence Agreement.

The USER agrees that it will not translate, alter, decompile, disassemble, reverse engineer, reverse compile, attempt to derive or reproduce any code from AA.

Disclaimer

MRC makes no representation or warranty with respect to AA and specifically disclaims any implied warranties of merchantability and fitness for a particular purpose or that use of MIX will not infringe any third party rights.

MRC reserves the right to revise AA and to make changes therein from time to time without obligation to notify any person or organisation of such revision or changes.

While MRC will make every effort to ensure the accuracy of AA, neither MRC nor its employees or agents may be held responsible for errors, omissions or other inaccuracies or any consequences thereof. The MRC will not be liable in any way for any losses howsoever caused by the use of AA, such losses to include but not be limited to loss of profit, business interruption, loss of business information, or other pecuniary loss, including but not limited to special incidental consequential or other damages.

Requirements

The system has been tested on Linux, but should also run without major modification on other flavours of Unix. It will require significant modification to run on Windows.

You need Matlab 6 or 7 (or possibly earlier) and SPM 5.

To use the parallel system you will need the LoadShare load balancing script.

Download

By downloading, you agree to the license agreement at the top of this page.

From version 2.1 onwards, aa development will use subversion.

You may download the latest release (see directory "tags") or development (see "trunk") version from http://imaging.mrc-cbu.cam.ac.uk/svn/aa

Version 2.2 http://imaging.mrc-cbu.cam.ac.uk/svn/aa/versions/release-2.2/

It would probably be easiest for you to use subversion to take a copy of these repositories, for example with something like:

  svn co http://imaging.mrc-cbu.cam.ac.uk/svn/aa/versions/release-2.2/

Version 2.0 is here: [ask] Version 1.2 is here: [ask] Version 1.1 is here: [ask]

Older versions are available from http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/download.htm

Installation outside CBU

Once you have downloaded and unpacked the aa directory, you'll need to change the following files. [aaroot] should be replaced with the path where you've put aa (e.g., /imaging/local/spm/aa at the CBU)

To use the parallel functionality, you will need a LoadShare spm wrapper or some other tool that allows SPM.

File [aaroot]/aa_ver11.m

Change path to point to your aa installation. You should also copy or symbollically link this file into some directory that is on your Matlab search path, or add the [aaroot] directory as a matlab path (with addpath('[aaroot]') where [aaroot] should be replaced with where you've put aa.

File [aaroot]/aa_engine/aas_getsubjpath.m

The default subject directory filenames created by aa are truncated. The raw data arrive from the scanner (via a DICOM gateway) with names like CBU060500_CBU060500/20060606_154324, which is rather redundant. They are truncated to CBU060500. This is done by this subroutine, when aap.directory_conventions.subject_directory_format=1 (the default).

You must either:

• change the default for aap.directory_conventions.subject_directory_format in your user script or the aap_directory_conventions parameter set
• modify the code in aas_getsubjpath.m to manipulate your filenames in the way you desire

File [aaroot]/aa_modules/aamod_autoidentifyseries.m

This initialisation module searches the raw datasets for specific series types. On our site:

• the structural is detected because it has the series name containing CBU_MPRAGE

• the fieldmap phase and magnitude have the protocol name of CBU_GREFIELDMAPPING

• real time t-maps are identified because they have the directory name EvaSeries_tTest

You must change these so that they are appropriate for your site.

File [aaroot]/aa_recipes_and_paramtersets/aap_directory_conventions_ver00.m

This specifies where various files should be retrieved from or placed. You must change the following lines:

% Raw data source BR aap.directory_conventions.rawdatadir='/mridata/cbu/'; BR % Central store for raw structurals BR aap.directory_conventions.centralstore_structurals='/imaging/local/structurals/cbu'; BR % Template for non skull-stripped normalisation BR aap.directory_conventions.T1template='/imaging/local/spm/spm5/templates/T1.nii'; BR

If you change code to re-instate skull stripped normalisation you will also need to modify

% Central store for skull-stripped structurals BR aap.directory_conventions.centralstore_ssstructurals='/imaging/local/structurals/cbu/skull_stripped'; BR % Template for skull-stripped normalisation BR aap.directory_conventions.T1sstemplate='/imaging/local/spm/spm99/templates/sbrain_avg152T1.img'; BR