112013-03-07 21:22:59localhostconverted to 1.6 markup102006-06-05 09:43:09RhodriCusack92006-06-05 09:42:26RhodriCusack82006-06-05 09:42:05RhodriCusack72006-06-05 09:41:36RhodriCusack62006-06-05 09:40:35RhodriCusack52006-06-05 09:40:15RhodriCusack42006-06-05 09:39:23RhodriCusack32006-06-05 09:39:00RhodriCusack22006-06-05 09:38:45RhodriCusack12006-06-05 09:38:27RhodriCusackThis 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

The data from our scanner, via a dicom gateway, get written in the following structure. /mridata/cbu/CBU[session number]_CBU[session number]/[sessionstarttime]/Series_[number]_[protocol name] e.g., /mridata/cbu/CBU060500_CBU060500/20060505_153428/Series_003_CBU_EPI_Standard Users outside Cambridge will probably find their data are written in a different format, and the protocol names are different. This will require a few changes to the aa code - see AutomaticAnalysisInstallation on how to make these You may change the location of raw data by changing the aap.directory_conventions.rawdatadir

While some control is provided over naming conventions, the file structure for processed data is essentially fixed. For each subject, the format is[aap.acq_details.root]/[subject name] e.g., /imaging/rhodri/mystudy/CBU060100 within each subject directory you will typically find the following subdirectories structurals stores processed structural (i.e., hires T1 weighted) imagesrealtime_tmaps stores converted real time t maps (if present) in nifti format[named session] one directory for each session, with name as provided for sessions in user script. Contains raw and processed EPIs in NIFTI formatresults stores first level statistical model (if used)within the study directory you will find rfx second level analysis, if used

Various aa specific files are written into this directory structure. In study root: aap_parameters.mat the aap structure corresponding to the user script last run on this studydone_[module name]diagnostic_[module name]Each module specifies the level at which it should be run (e.g., once per study, per subject, or per session). The done_ and diagnostic_ files for a module will then get written to the appropriate study, subject or session directory.