AutomaticAnalysisInstallation - MRC CBU Imaging Wiki

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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