Reference

Available recipes

Name:

aarecipe_general_ver01

Description:

Standard recipe

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

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

directory_conventions

Parameter set

Description

aap_directory_conventions_ver00

Example fields:
Sub-directories called "realtimetmaps", “structurals”
Raw data in /mridata/cbu
Central store for structurals /imaging/local/data/structurals/cbu
Central store for skull-stripped structurals
/imaging/local/data/structurals/cbu/skull_stripped
Template for normalisation /imaging/local/spm/spm5/templates/T1.img

options

Parameter set

Description

aap_options_ver00

Example fields:
Provide fairly verbose output while running script.
Automatically identify field maps and structurals in datasets.
Copy structurals to central directory.

tasklist

Parameter set

Description

aap_tasklist_cbudefault_ver00

Task list:
aamod_newsubj_init
aamod_autoidentifyseries
aamod_copyfieldmaps
aamod_pvconv
aamod_copystructural
aamod_ana4dto3d
aamod_slicetiming
aamod_realign
aamod_undist
aamod_coreg'
aamod_norm
aamod_undist_reslice

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

spmanalysis

Parameter set

Description

aap_spmanalysis_tr1p1_ver00

Example settings:
TR=1.1; slicetime=0.0762; smoothing FWHM=10mm

acq_details

Parameter set

Description

aap_spmanalysis_tr1p1_ver00

Settings mostly overridden by aap_user

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;

More expansive help is within the parameter set files themselves (e.g., type edit aap_acq_details_ver00)

acq_details

see AutomaticAnalysisManual section 4.4 for notes on filling these fields

Field

Typical value

Description

root

'/imaging/rhodri/newsimultaneous'

Path to directory where processed study will be stored. This directory should exist. Must be assigned by user.

subjects

Don't set manually: use aas_addsubject command

[stores subjects]

sessions

{'ns1_block1','ns1_block2','ns2_passive','ns2_active'};

List of sessions. Must be assigned by user

brukersessionnums

Don't set manually: use aas_addsubject command

[List of session numbers - apologies for legacy 'bruker']

ignoreseries

Don't set manually: use aas_addsubject command

[List of sessions to be ignored by auto scan code, useful if you have multiple structurals]

fieldmaps

[9 11;9 11; 9 12]

Session number of fieldmaps. Automatically detected by default

newfieldmap

[8; 7; 4]

Automatically detected by default

numdummies

18

Number of dummy scans at the start of each session. Must be assigned by user.

structural

{}

Session number of structurals. Automatically detected by default

tmaps

{[3 4],[5 7]}

Session numbers for real time t-maps

specialseries

{[3 4],[5 6]}

Series to be dicom converted only

directory_conventions

Field

Typical value

Description

four_d_dir

'4d_files'

Name of subdirectory in subject directory for 4d analyze files from pvconv.pl

proc_fieldmaps

'proc_fieldmaps'

Name of subdirectory in subject directory for processed fieldmaps

raw_fieldmaps

'raw_fieldmaps'

Name of subdirectory in subject directory for raw fieldmaps

structdirname

'structurals'

Name of subdirectory in subject directory for structurals

rawdatadir

'/imaging/local/wbic_data/'

Where raw data are

centralstore_structurals

'/imaging/local/data/structurals'

Where structurals should be put

centralstore_ssstructurals

'/imaging/local/data/structurals/skull_stripped'

Where to find and put skull stripped structurals

T1sstemplate

/imaging/local/spm/spm99/templates/ sbrain_avg152T1.img

Template file for normalisation

subject_directory_format

0: manually specify in aap.directory_conventions.subject_directory_names
1: truncated subject names (e.g., W020123) {default}
2: automatically generated ordinal labels for subject directories (S01, S02, S03...)

Format for subject output directories

subject_filename_format

0: manually specify in field aap.directory_conventions.subject_filenames
1: truncated subject names (e.g., W020123) {default}
2: automatically generated ordinal labels for subject directories (S01, S02, S03...)

Format for subject directories

subject_directory_names

{‘myfirstsubjdir’,’blob’}

Manually specified names of directories for subjects

subject_filenames

{‘myfirstsubjfilename’,’blob’}

Manually specified names of EPI filenames for subjects

options

Field

Typical value

Description

verbose

1

Give user regular updates of status when running tool

copystructuraltocentralstore

1

Copy structurals to central store

deletestructuralaftercopyingtoc

1

Delete local copy of structural (before skull stripping) after copying to central store

autoidentifystructural

1

Automatically find structurals in raw datasets

autoidentifyfieldmaps

1

Automatically find fieldmaps in raw datasets

spmanalysis

Field

Typical value

Description

TRs

1.1

Repetition time

slicetime

0.0762

Time to acquire a single slice

refslice

1

Reference slice for slice timing

FWHM

10

Smoothing kernel (mm)

evoltime

9.104

Evolution time of field maps

structuralbetf

0.5

Bet fractional threshold value to be used when skull stripping tb_ files

tasklist

Field

Typical value

Description

initialisationmodules

{'aamod_checkparameters' 'aamod_make_subjects_short' 'aamod_autoidentifyseries'}

List of initialisation modules, which are always run during processing

stages

{'aamod_newsubj_init', 'aamod_autoidentifyseries', 'aamod_copyfieldmaps', 'aamod_pvconv', 'aamod_copystructural', 'aamod_ana4dto3d', 'aamod_slicetiming', 'aamod_realign', 'aamod_undist', 'aamod_coreg', aamod_norm', 'aamod_undist_reslice'}

List of modules to be called to perform processing. These are only run once each (i.e., if there is no file done_xxx)

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).

aamod_checkparameters.m

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

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.

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.

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