This manual is for aa parallel version 2.2 and earlier. You might prefer the new aa wiki for aa version 3.0 and above or information on cloud execution
Contents
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: |
options
Parameter set |
Description |
aap_options_ver00 |
Example fields: |
tasklist
Parameter set |
Description |
aap_tasklist_cbudefault_ver00 |
Task list: |
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: |
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 |
Format for subject output directories |
subject_filename_format |
0: manually specify in field aap.directory_conventions.subject_filenames |
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