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Manual reference
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:
e.g., aap.directory_conventions.rawdatadir = ’/imaging/rhodri/my_raw_data';
| parameters | description | type | options |
|---|---|---|---|
| aap | |||
| aap.directory_conventions | |||
| aap.directory_conventions.fieldmapsdirname | Subdirectory in subject dir for fieldmaps | text | |
| aap.directory_conventions.structdirname | Subdirectory in subject dir for MRI structurals | text | |
| aap.directory_conventions.tmapsdirname | Subdirectory in subject dir for real-time T maps | text | |
| aap.directory_conventions.specialseriesdirname | Subdirectory in subject dir for special series | text | |
| aap.directory_conventions.eventsdirname | Subdirectory in study, subject and/or session for event files | text | |
| aap.directory_conventions.rawdatadir | Subdirectory to find raw MRI data | dir | |
| aap.directory_conventions.rawmegdatadir | Directory to find raw MEG data | dir | |
| aap.directory_conventions.centralstore_structurals | Location of central store for structruals | dir | |
| aap.directory_conventions.T1template | Location of T1 template | dir | |
| aap.directory_conventions.centralstore_ssstructurals | Location of central store for skull stripped structurals | dir | |
| aap.directory_conventions.T1sstemplate | Location of skull-stripped T1 template | dir | |
| aap.directory_conventions.rawdataafterconversionprefix | Prefix of raw data after conversion from DICOM to NIFTI | text | |
| aap.directory_conventions.subject_directory_format | Format of subject directory | optionlist | CBU060500S01 |
| aap.directory_conventions.subject_filenames_format | Format of filenames within session directory | optionlist | CBU060500S01 |
| aap.directory_conventions.rawseries_usefileorder | In raw data, use number in file listing not filtering by series number | ||
| aap.directory_conventions.selectechonumbers | Which echo numbers? | vector_array | |
| aap.directory_conventions.reportname | Name of output from aa_report | file | |
| aap.directory_conventions.stats_singlesubj | Directory for single subject statistics | dir | |
| aap.directory_conventions.rfx | Directory for random effects statistics | dir | |
| aap.directory_conventions.dartelsubjdirname | Name of DARTEL subject directory | dir | |
| aap.directory_conventions.outputformat | Determnes format of output - currently empty, or splitbymodule | ||
| aap.directory_conventions.analysisid | Analysis ID | ||
| aap.directory_conventions.seriesoutputformat | sprintf formatting string to get series directory from number - at CBU is Series_%03d*; at CABI *_%d | text | |
| aap.directory_conventions.seriesnamingconvention | Used by aas_getseriesnumber to choose naming convention of incoming data - CBU= Series_003_MPRAGE; CABI= fmri_3_4 | optionlist | CABI |
| aap.options | |||
| aap.options.verbose | How verbose to be | yesno | |
| aap.options.copystructuraltocentralstore | Copy structurals to central store? | yesno | |
| aap.options.deletestructuralaftercopyingtocentralstore | Delete local copy of structurals | yesno | |
| aap.options.autoidentifystructural | Automatically identify structurals? | yesno | |
| aap.options.autoidentifystructural_chooselast | Automatically select last of structurals when there is more than one? | yesno | |
| aap.options.autoidentifystructural_average | Average across structurals when there is more than one? | yesno | |
| aap.options.autoidentifyfieldmaps | Automatically identify field maps? | yesno | |
| aap.options.autoidentifytmaps | Automatically identify t maps? | yesno | |
| aap.options.aa_minver | Minimum allowed aa version | double | |
| aap.options.aa_maxver | Maximum allowed aa version | double | |
| aap.options.userinterface | User interface for checking and specifying task parameters | yesno | |
| aap.options.processinglocation | Where processing should happend - local vs. aws | ||
| aap.acq_details | |||
| aap.acq_details.root | Root path for processed data | dir | |
| aap.acq_details.numdummies | Number of dummy scans | int | |
| aap.acq_details.topscannumber | Ignore EPI scans after this one | int | |
| aap.acq_details.subjects | Subject details | ||
| aap.acq_details.sessions | Functional sessions | ||
| aap.timeouts | |||
| aap.timeouts.starting | timeout period for spm startup (mins) | ||
| aap.timeouts.joballocated | timeout period for worker prepare (mins) | ||
| aap.timeouts.busy | timeout period for worker job (mins) | ||
| aap.timeouts.bored | timeout period for bored worker (mins) | ||
| aap.tasksettings | |||
| aap.tasksettings.aamod_checkparameters | Check user parameters | ||
| aap.tasksettings.aamod_evaluatesubjectnames | Check raw data | ||
| aap.tasksettings.aamod_make_subjects_short | Make short subject filenames | ||
| aap.tasksettings.aamod_autoidentifyseries_timtrio | Automatically identify series numbers | ||
| aap.tasksettings.aamod_study_init | aa initialise study | ||
| aap.tasksettings.aamod_newsubj_init | Create subject directory | ||
| aap.tasksettings.aamod_converttmaps | Converting any real time t maps | ||
| aap.tasksettings.aamod_copystructural | Copying structural | ||
| aap.tasksettings.aamod_convert_epis | Convert EPIs | ||
| aap.tasksettings.aamod_realign | SPM motion correction | ||
| aap.tasksettings.aamod_tsdiffana | run tsdiffana | ||
| aap.tasksettings.aamod_slicetiming | SPM slice timing | ||
| aap.tasksettings.aamod_coreg_noss | SPM coregistration | ||
| aap.tasksettings.aamod_norm_noss | SPM normalise estimate parameters | ||
| aap.tasksettings.aamod_norm_write | SPM normalisation write | ||
| aap.tasksettings.aamod_smooth | SPM smooth |
These modules are run every time aa_doprocessing is called, which is different from standard modules 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.
THIS IS NO LONGER AN INITIALISATION MODULE, BUT A FULL MODULE TO BE ADDED TO YOUR TASKLIST. 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 thereafter.
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.
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.
