AutomaticAnalysisManual

Overview

This specifies an analysis. Many studies can be analysed up to and including the stage of normalisation with changes to this alone. With some changes to the specificaiton of the experimental design in aamod_model_firstlevel, you may run all the way up to and including second level statistics.

There are sections to the user script:

	Section	Probability you need to change it and when
1	Choosing a recipe	(0.2) If you use a non-standard acquisition sequence or wish to do a quite different type of analysis
2	Changing any of the parameter sets in the recipe	(0.1) If you wish to change a single parameter set controlling part of the automatic processing from what is specified in a recipe
3	Initialising using the parameter sets	(0.01) Usually never
	Setting study specific details	(1.0) Always
	Set any other parameters that need to differ from the defaults	(0. If you wish to change single parameters

||<style="vertical-align: top;">

Calling aa_doprocessing to do the processing

(0.01) Usually never

An example, which will process 3 subjects each with sessions up to and including normalisation is below:

% Automatic analysis

% User master script

% Rhodri Cusack MRC CBU Cambridge 200

% (1) RESET ALL PARAMETERS

aap=[];

% (2) ANALYSIS RECIPE

% General auto TR recipe; slice order Siemens product sequence default

aap=aarecipe_general_ver01(aap);

% (3) MODIFY STANDARD RECIPE MODULE SELECTION HERE IF YOU'D LIKE

% do this here

% ( GET ALL THE PARAMETERS FOR THIS RECIPE

aap=aa_init(aap);

% ( DEFINE STUDY SPECIFIC PARAMETERS

aap.options.aa_minver=1.0; % will only work on aa version 1.0 or above

% The study directory

aap.acq_details.root = '/home/rhodri/pvs/cbu';

% Add subjects and session numbers for EPI data

aap=aas_addsubject(aap,'*CBU0011/*',[11 12]);

aap=aas_addsubject(aap,'*CBU0012/*',[12 10]);

% Condition names for each session, must be same for all subjects

aap.acq_details.sessions={'mystery1','mystery2'};

% Number of dummy scans at the start of each session

aap.acq_details.numdummies=18;

% ( SET ANY OTHER PARAMETERS YOU WOULD LIKE TO BE DIFFERENT FROM THE DEFAULTS

% (7) SET ANY SPM DEFAULTS IF NEEDED

aap.spm.defaults.normalise.write.vox=[3 3 3];

% (8) DO PROCESSING

aa_doprocessing(aap);

The four sections you are mostly likely to need to change (1, 2, and are now discussed in turn.

NB: Be careful about changing the aa_user script after you’ve run part of an analysis. The problem with doing this is that if the changes you make would have affected the parts that have already been completed, you won’t be able to use the script to exactly recreate your data in future.

Choosing the recipe

These are chosen with the line

aap=[recipename](aap);

e.g., aap=aarecipe_general(aap);

An example recipe is shown below. Descriptions of the parameter sets are in the next section. A full list of recipes is on the AutomaticAnalysisManualReference page.

Name:		aarecipe_general
Description:	Standard automatic TR recipe
Parameter set choice:
Type	Parameter set
directory_conventions	aap_directory_conventions_ver00
options	aap_options_ver00
tasklist	aap_tasklist_cbudefault_ver00
spmanalysis	aap_spmanalysis_tr1p1_ver00
acq_details	aap_acq_details_ver00

Modify parameter set selection

A recipe comprises a description of the parameter sets that should be included. Once you’ve chosen a recipe you may override some of the different parameter sets. You would do this in stage 2 of the user script (see above) with a line like

aap.recipe.directory_conventions=’aap_directory_conventions_mynewstyle’

(NB: no ‘.m’ on end)

There are different types of parameter sets. A full list of the available parameter sets is given in the AutomaticAnalysisManualReference section.

Type	Description
directory_conventions	Specifies directory and file conventions, for example: raw data directory (by default /mridata/cbu)
options	General aa program options, for example: whether to automatically identify the field maps and structurals in the incoming dataset; whether to copy structurals to the central store
tasklist	The list of tasks to be performed (e.g., modules to be executed) for each study
spmanalysis	SPM & imaging analysis parameters, for example: TR & slice acquisition tim; smoothing FWHM; evolution time of fieldmaps
acq_details	Acquisition details. Several of the defaults are overridden in the user script, for example: - study directory - subject list

Setting your acquisition parameters

You always need to do this, to tell the system which files to analyse. The essential lines with explanation and notes are these:

aap.acq_details.root = '/cbu/scratch2/rhodri.cusack/newsimultaneous';	Specifies the directory where the processed study data are stored. This directory should exist before you run the script.
aap.acq_details.sessions={'ns1_block1','ns1_block2','ns2_passive','ns2_active'};	These are names of the blocks in your experiment. This must be the same for all subjects. Here, there were four blocks. I find it easiest to use intuitive names that describe the behavioural condition.
aap.acq_details.numdummies=18;	Number of dummy scans at the start of each session that need to be thrown away.

Too make it easy to see the correspondence between subject and session number, I now recommend subject names are added with the aas_addsubject command:

aap=aas_addsubject(aap, ‘*CBU0011\*’,[11]);

The full syntax of this command is in Error! Reference source not found., but the first string specifies the raw data for this subject (you may use wildcards) and the numbers in square brackets the series numbers for the EPI data. There should be as many of these are there are blocks, as specified in aap.acq_details.sessions and described above.

By default, MPRAGE structural and GRE_FIELDMAPPING fieldmap scans are automatically detected. This will lead to an error if for some reason you have collected more than one fieldmap or structural scan for a given subject. In this case you can specify those scans which should be ignored in a final optional parameter. For example, if you wished to ignore aborted structural scans with series numbers 2 and 3, you might type:

aap=aas_addsubject(aap, ‘*CBU0011\*’,[11],[2 3]);

Set specific parameters that you wish to differ from the defaults

Once you’ve set up the parameters using a recipe and any different parameter sets you’d like, there may still be one or two parameters that you need to change. You do this at this stage. For example, in the sample script, if my data were no longer in /mridata/cbu I would add the line:

aap.directory_conventions.rawdatadir='/imaging/rhodri/newsimultaneous';

A full list of parameters with descriptions is given in section Error! Reference source not found..

Set any SPM defaults

Any SPM defaults can be changed. You do this using lines like the following: