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Command reference
Mike Jones edited this page Jun 3, 2022
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The following table includes aap structure fields that are often set in the userscript or parameter file, organized by type.
| 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 |
Contents
- Home
- Tutorial Introduction
- Installation
- Parameter File Setup
- Pipeline Specification
- Statistical Modelling
- Working with Streams
- DICOM and NifTi Input
- Branched Tasklists
- Connecting Pipelines
- Cluster Processing
- Diffusion Analysis
- A.0 - Frequently Asked Questions
- A.1 - aap Struct Fields
- A.2 - Module List
- A.3 - Example Scripts
- A.4 - Integrated Third Party Tools
- A.5 - Module Development Guide