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=== 1.5.1 aamod_newsubj_init.m ===
Makes the subject directory if it doesn’t exist already.

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=== aamod_copyfieldmaps.m ===
Copies the raw fieldmaps to the specified “rawphase” directory. The data in this directory will be used by undistort to reconstruct the raw data into processed fieldmaps.

||=== aamod_pvconv.m ||[no longer used] === ||


Script to convert the raw Siemens DICOM data files (generally located in /mridata).

=== aamod_convertseries.m ===
Converts EPI data from Siemens DICOM to NIFTI format.

=== 1.5.4 aamod_converttmaps.m ===
Converts realtime t maps into NIFTI format and puts them into folder realtime_tmaps in each subject directory

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=== 1.5.5 aamod_copystructural.m ===
Copies the structural to the central unit storage place for structurals (currently /imaging/local/data/structurals).

=== 1.5.6 aamod_ana4dto3d.m [no longer used] ===
Converts the 4dfiles (output of pvconv) to many 3d files. Done on EPI sessions (as you are acquiring multiple volumes across time). You will have as many 3d files in your session as there are TRs (or volumes) in the session. Optional output includes the mean image, the mean variance image, and the variance slice. These are helpful diagnostic images. There is also the option to not write out the dummy scans (because they are simply there to let the scanner signal steady, and won't be included in your analysis).

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=== 1.5.7 aamod_slicetiming.m ===
Corrects for the staggered order of slice acquisition. This makes the data on each slice correspond to the same point in time. Otherwise the data on one slice could represent a point in time as far removed as 1/2 the TR from an adjacent slice. Generally one uses sinc interpolation.

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=== 1.5. aamod_realign.m ===
Causes all of the volumes in each session to be registered to the first volume in that session, then all volumes are registered to the first volume of the first session. So, for each session, you get a mat file with the parameters to register all the slices in that session to the first slice in that session. You also get an overall .mat file with all the parameters in relation to the first scan/first volume. This overall mat file is in your first session folder.

You will also get a text file of the realignment parameters--this will be used by SPM during model estimation to get rid of signal due to movement.

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=== 1.5. aamod_undist.m ===
Creates processed fieldmaps (placed in the processed fieldmaps directory), which are then used to correct distortions in the EPIs. This improves normalization and statistical power.

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=== 1.5. aamod_coreg.m ===
Puts the selected scans (usually the mean EPI image and the structural) in the same space. Usually one coregisters the structural to the mean EPI image (without reslicing), as this requires reorienting only one structural, as opposed to hundreds of EPIs.

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=== 1.5.1 aamod_norm.m ===
Transforms the scans into standardised space (given by a template image). One can skull-strip and normalize the structurals to a T1 template, then apply the parameters derived by the normalization to the EPIs. Or one can try masked EPI normalization, in which masks are created for areas of signal dropout in the EPI, and then the EPIs are normalized to an EPI template.

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=== 1.5.1 aamod_undist_reslice.m ===
Helpful script that writes out the realigned-undistorted-normalized-smoothed images (or just up to normalized, with no smoothing). Saves one from having to write out the EPI images for each of the aforementioned stages individually, by combining all these processes in one resampling step.
For help on individual modules, you should now go to these automatically generated pages http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/html

Include(AutomaticAnalysisTopbar)



Reference

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Available recipes

Name:

aarecipe_standard_tr1p1_ver00

Description:

Standard TR=1.1s 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

*** need sparse, ISS ***

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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

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

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 help on individual modules, you should now go to these automatically generated pages http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/html

Helper functions

aas_addsubject

SYNTAX:

aap=aas_addsubject(aap,’subject file name’,[EPI series number 1, EPI series number 2,...]);

EXAMPLE

aap=aas_addsubject(aap,’*CBU050011/*’,[5 11]);

DESCRIPTION

This function adds the details of a subject to be analysed. The file name of the raw data and EPI session numbers are specified.

You may use filename wildcard characters (*) in the subject directory name.

||By default, the raw data is searched for in /mridata/cbu/ (add line like

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

to user script – see 4.3

The EPI series number should be that of the raw data series directories with names similar to

Series_004_CBU_EPI_Std_RealTime_30s

or

Series_002_CBU_EPI_Standard

aa_benchmark

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

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