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

= 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.

= 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)

== 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 on 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
aap.directory_conventions.rawdatadir='/mridata/cbu/';
% Central store for raw structurals
aap.directory_conventions.centralstore_structurals='/imaging/local/structurals/cbu';
% Central store for skull-stripped structurals
aap.directory_conventions.centralstore_ssstructurals='/imaging/local/structurals/cbu/skull_stripped';
% Template for skull-stripped normalisation
aap.directory_conventions.T1sstemplate='/imaging/local/spm/spm99/templates/sbrain_avg152T1.img';
% Template for non skull-stripped normalisation
aap.directory_conventions.T1template='/imaging/local/spm/spm5/templates/T1.nii';