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Reference

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Available recipes

To see parameter set choices go to this page in the m2html help: http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/html/aa_recipes_and_parametersets/aarecipe_general_ver01.html

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Available parameter sets

To see the full list of settings in a parameter set, at the Matlab prompt type:

>> edit [parameter set name]

e.g.,

>> edit aap_directory_conventions_ver00

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directory_conventions

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options

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tasklist

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See description of the aa version after 1.1 for a new way of specifying tasklists using the aas_addtask command.

spmanalysis

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acq_details

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Individual parameters

Here is a list of the individual parameters. They are divided into sections, by their type (shown in bold). To fill a field, in section 5 of your user script, put:

aap.[type].field=[value];

For example,

aap.directory_conventions.rawdatadir=’/imaging/rhodri/my_raw_data;

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acq_details

% The study directory 
aap.acq_details.root = '';

%   Condition names for each session, assumed same for each subject
aap.acq_details.sessions={};

% If aap.directory_conventions.selectechonumbers is true, then you must
% specifiy which echo numbers should be selected for each session in here
aap.acq_details.sessions_echonumbers=[];

% Don't set these manually - use aas_addsubject command as in example user script
%   *the subject directories
aap.acq_details.subjects={};
%   *Bruker (Scanning) session numbers: these correspond to condition names above
aap.acq_details.brukersessionnums={};

% session numbers of any series to be ignored in the analysis [djm 20/3/06]
aap.acq_details.ignoreseries={};

% Number of dummy scans at the start of each session
aap.acq_details.numdummies=0;

% Bruker session numbers for phase maps (1a, 1c - don't need to specify 1b)
%  can be left blank, and will be filled automatically if
%  aap.options.autoidentifyfieldmaps=1
aap.acq_details.fieldmaps=[];

% Blank structure for new fieldmaps
%  can be left blank, and will be filled automatically if
%  aap.options.autoidentifyfieldmaps=1
aap.acq_details.newfieldmap=[];

% Series numbers for structurals - put [] if one wasn't acquired
%  can be left blank, and will be filled automatically if
%  aap.options.autoidentifystructural=1
aap.acq_details.structural={};

% Series numbers for real time t maps - put [] if one not needed
%  can be left blank, and will be filled automatically if
%  aap.options.autoidentifytmaps=1
aap.acq_details.tmaps={};

% Special series to be converted from DICOM and put in specialseries folder
aap.acq_details.specialseries={};

% Max number of scans
aap.acq_details.topscannumber=[];

directory_conventions

options

spmanalysis

tasklist

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Initialisation modules

These modules are run every time aa_doprocessing is called, which is different from standard modules (see Error! Reference source not found.) which are only executed if they haven’t already been done (as recorded by a “done_” flag).

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aamod_checkparameters.m

Check that no new fields have been created in the aap structure by the user to trap mis-typing.

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aamod_make_subjects_short

EPI filenames are short versions of subject number – either session code (e.g., CBU030207) or ordinal labels (e.g., S03) if specified in directory_conventions. This module makes these shorter filenames.

aamod_evaluatesubjectnames

Evaluates any wildcards in the subject names.

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aamod_autoidentifyseries.m

Identifies data series in the raw data that correspond to fieldmaps, MPRAGE structurals and realtime T maps. For speed, stored in .mat file in subject directory the first time, and loaded from this.

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Modules & helper functions

All of the work is done by a set of modules, each of which performs an individual processing stage. These modules are described below. Each will only be executed if they haven’t been done already, as signified by a “done_” flag (see Error! Reference source not found., Error! Reference source not found.)

For a reference guide to individual modules (see aa_modules) and helper functions (see aa_engine), you should now go to these automatically generated pages http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/html

aa_benchmark

Tells you how long each stage took to run (in seconds).

aa_report

Produces a HTML report describing your study