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
aap.directory_conventions.rawdatadir='/mridata/cbu/';
% Central store for raw structurals
aap.directory_conventions.centralstore_structurals='/imaging/local/structurals/cbu';
% Template for non skull-stripped normalisation
aap.directory_conventions.T1template='/imaging/local/spm/spm5/templates/T1.nii';
If you change code to re-instate skull stripped normalisation you will also need to modify
% 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';