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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

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';