<> ---- . ''' 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:<
>Sub-directories called "realtimetmaps", “structurals”<
>Raw data in /mridata/cbu<
>Central store for structurals /imaging/local/data/structurals/cbu<
>Central store for skull-stripped structurals<
>/imaging/local/data/structurals/cbu/skull_stripped<
>Template for normalisation /imaging/local/spm/spm5/templates/T1.img<
> || <> === options === ||''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. || <> === tasklist === ||''Parameter set'' ||''Description'' || ||aap_tasklist_cbudefault_ver00 ||Task list: <
>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 || <> 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:<
>TR=1.1; slicetime=0.0762; smoothing FWHM=10mm<
> || <> === 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<
> 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 || === 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