402013-03-07 21:23:53localhostconverted to 1.6 markup392007-08-29 18:22:58RhodriCusack382007-08-29 18:21:20RhodriCusack372007-08-29 18:15:46RhodriCusackRevert to revision 35.362007-08-29 18:13:50RhodriCusack352007-08-29 18:10:21RhodriCusack342007-08-29 18:09:28RhodriCusack332006-07-29 14:10:49RhodriCusack322006-07-29 14:10:29RhodriCusack312006-07-04 22:39:38DorisEckstein302006-07-04 22:29:29DorisEckstein292006-07-04 22:25:12DorisEckstein282006-06-22 13:19:35RhodriCusack272006-06-05 13:31:40RhodriCusack262006-06-05 13:31:09RhodriCusack252006-06-05 13:29:20RhodriCusack242006-06-02 11:34:57RhodriCusack232006-06-02 10:55:54RhodriCusack222006-06-02 10:45:01RhodriCusack212006-06-02 00:49:41RhodriCusack202006-06-02 00:35:11RhodriCusack192006-06-02 00:28:30RhodriCusack182006-06-02 00:27:56RhodriCusack172006-06-02 00:25:00RhodriCusack162006-06-02 00:21:08RhodriCusack152006-06-02 00:18:19RhodriCusack142006-06-02 00:14:28RhodriCusack132006-06-02 00:13:54RhodriCusack122006-06-02 00:13:27RhodriCusack112006-06-02 00:10:07RhodriCusack102006-06-02 00:08:51RhodriCusack92006-06-01 23:58:22RhodriCusack82006-06-01 23:56:03RhodriCusack72006-06-01 23:52:42RhodriCusack62006-06-01 23:52:01RhodriCusack52006-06-01 23:50:20RhodriCusack42006-06-01 23:44:59RhodriCusack32006-06-01 23:44:33RhodriCusack22006-06-01 23:43:24RhodriCusack12006-06-01 23:41:20RhodriCusackThis 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 Introduction General overview File format Choosing an appropriate recipe Getting started aa parallel Parameter set reference Release notes for different versions Contents

Name: aarecipe_general_ver01 Description: Standard recipe To see parameter set choices go to this page in the m2html help:

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

Parameter set Description aap_directory_conventions_ver00 Example fields:Sub-directories called "realtimetmaps", “structurals”Raw data in /mridata/cbuCentral store for structurals /imaging/local/data/structurals/cbuCentral store for skull-stripped structurals/imaging/local/data/structurals/cbu/skull_strippedTemplate for normalisation /imaging/local/spm/spm5/templates/T1.img

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.

Parameter set Description aap_tasklist_cbudefault_ver00 Task list: aamod_newsubj_initaamod_autoidentifyseriesaamod_copyfieldmapsaamod_pvconvaamod_copystructuralaamod_ana4dto3daamod_slicetimingaamod_realignaamod_undistaamod_coreg'aamod_normaamod_undist_reslice See description of the aa version after 1.1 for a new way of specifying tasklists using the aas_addtask command.

Parameter set Description aap_spmanalysis_tr1p1_ver00 Example settings:TR=1.1; slicetime=0.0762; smoothing FWHM=10mm

Parameter set Description aap_spmanalysis_tr1p1_ver00 Settings mostly overridden by aap_user

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)

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

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

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

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

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)

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).

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

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.

Evaluates any wildcards in the subject names.

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.

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

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

Produces a HTML report describing your study