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 ''' Contents ''' [[TableOfContents]]
  . ''' Contents ''' [[TableOfContents]]
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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		 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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||<style="vertical-align: top;">subject_directory_format ||<style="vertical-align: top;"> 0: manually specify in aap.directory_conventions.subject_directory_names[[BR]] 1: truncated subject names (e.g., W020123) {default}[[BR]] 2: automatically generated ordinal labels for subject directories (S01, S02, S03...)[[BR]][[BR]] ||<style="vertical-align: top;">Format for subject output directories||
||<style="vertical-align: top;">subject_filename_format ||<style="vertical-align: top;"> 0: manually specify in field aap.directory_conventions.subject_filenames[[BR]] 1: truncated subject names (e.g., W020123) {default}[[BR]] 2: automatically generated ordinal labels for subject directories (S01, S02, S03...)[[BR]] ||<style="vertical-align: top;">Format for subject directories||
||<style="vertical-align: top;">subject_directory_names[[BR]] ||<style="vertical-align: top;">{‘myfirstsubjdir’,’blob’} ||<style="vertical-align: top;">Manually specified names of directories for subjects||		 ||<style="vertical-align: top;">subject_directory_format ||<style="vertical-align: top;"> 0: manually specify in aap.directory_conventions.subject_directory_names[[BR]] 1: truncated subject names (e.g., W020123) {default}[[BR]] 2: automatically generated ordinal labels for subject directories (S01, S02, S03...)[[BR]][[BR]] ||<style="vertical-align: top;">Format for subject output directories ||
||<style="vertical-align: top;">subject_filename_format ||<style="vertical-align: top;"> 0: manually specify in field aap.directory_conventions.subject_filenames[[BR]] 1: truncated subject names (e.g., W020123) {default}[[BR]] 2: automatically generated ordinal labels for subject directories (S01, S02, S03...)[[BR]] ||<style="vertical-align: top;">Format for subject directories ||
||<style="vertical-align: top;">subject_directory_names[[BR]] ||<style="vertical-align: top;">{‘myfirstsubjdir’,’blob’} ||<style="vertical-align: top;">Manually specified names of directories for subjects ||
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||<style="vertical-align: top;">refslice||<style="vertical-align: top;">1||<style="vertical-align: top;">Reference slice for alignment||
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||<style="vertical-align: top;">initialisationmodules ||<style="vertical-align: top;">{'aamod_checkparameters' 'aamod_make_subjects_short' 'aamod_autoidentifyseries'}[[BR]] ||<style="vertical-align: top;">List of initialisation modules, which are always run during processing|| ||<style="vertical-align: top;">initialisationmodules ||<style="vertical-align: top;">{'aamod_checkparameters' 'aamod_make_subjects_short' 'aamod_autoidentifyseries'}[[BR]] ||<style="vertical-align: top;">List of initialisation modules, which are always run during processing ||
||<style="vertical-align: top;">stages ||<style="vertical-align: top;">{'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'} ||<style="vertical-align: top;">List of modules to be called to perform processing. These are only run once each (i.e., if there is no file done_xxx) ||
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||<style="vertical-align: top;">stages ||<style="vertical-align: top;">{'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'} ||<style="vertical-align: top;">List of modules to be called to perform processing. These are only run once each (i.e., if there is no file done_xxx) ||


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Include(AutomaticAnalysisTopbar)

Reference

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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

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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

Parameter set

Description

aap_directory_conventions_ver00

Example fields:BRSub-directories called "realtimetmaps", “structurals”BRRaw data in /mridata/cbuBRCentral store for structurals /imaging/local/data/structurals/cbuBRCentral store for skull-stripped structuralsBR/imaging/local/data/structurals/cbu/skull_strippedBRTemplate for normalisation /imaging/local/spm/spm5/templates/T1.imgBR

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options

Parameter set

Description

aap_options_ver00

Example fields:BRProvide fairly verbose output while running script.BRAutomatically identify field maps and structurals in datasets.BRCopy structurals to central directory.

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tasklist

Parameter set

Description

aap_tasklist_cbudefault_ver00

Task list: BRaamod_newsubj_initBRaamod_autoidentifyseriesBRaamod_copyfieldmapsBRaamod_pvconvBRaamod_copystructuralBRaamod_ana4dto3dBRaamod_slicetimingBRaamod_realignBRaamod_undistBRaamod_coreg'BRaamod_normBRaamod_undist_reslice

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spmanalysis

Parameter set

Description

aap_spmanalysis_tr1p1_ver00

Example settings:BRTR=1.1; slicetime=0.0762; smoothing FWHM=10mmBR

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acq_details

Parameter set

Description

aap_spmanalysis_tr1p1_ver00

Settings mostly overridden by aap_userBR

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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

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

{'W030510.ls1' 'W030511.ls1' 'W030512.ls1'}

List of subjects. Must be assinged by user.

sessions

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

List of sessions. Must be assigned by user

brukersessionnums

{[4 5 8 7] [4 5 7 8] [4 5 8 7]}

List of session numbers. Must be assigned by user. [usually done with aas_addsubject command, see]

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.

structurals

{}

Session number of structurals. Automatically detected by default

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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_namesBR 1: truncated subject names (e.g., W020123) {default}BR 2: automatically generated ordinal labels for subject directories (S01, S02, S03...)BRBR

Format for subject output directories

subject_filename_format

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

Format for subject directories

subject_directory_namesBR

{‘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 alignment

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'}BR

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)

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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

CbuImaging: AutomaticAnalysisManualReference (last edited 2013-03-07 21:23:53 by localhost)