13103
Comment:
|
13170
|
Deletions are marked like this. | Additions are marked like this. |
Line 158: | Line 158: |
=== aa_report === Produces a HTML report describing your study |
Include(AutomaticAnalysisTopbar)
Contents TableOfContents
Reference
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 ***
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: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 |
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. |
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 |
spmanalysis
Parameter set |
Description |
aap_spmanalysis_tr1p1_ver00 |
Example settings:BRTR=1.1; slicetime=0.0762; smoothing FWHM=10mmBR |
acq_details
Parameter set |
Description |
aap_spmanalysis_tr1p1_ver00 |
Settings mostly overridden by aap_userBR |
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;
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 |
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) |
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