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= File Structure =

== Raw data ==
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]'' [[BR]]

''e.g., /mridata/cbu/CBU060500_CBU060500/20060505_153428/Series_003_CBU_EPI_Standard'' [[BR]]


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

== Processed data ==
While some control is provided over naming conventions, the file structure for processed data is essentially fixed. For each subject, the format is[[BR]]

''[processed data path]/[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) images[[BR]]
''realtime_tmaps''    - stores converted real time t maps (if present) in nifti format [[BR]]
''[named session]''   - one directory for each session, with name as provided for sessions in user script. Contains raw and processed EPIs in NIFTI format[[BR]]
''results''           - stores first level statistical model (if used)[[BR]]

within the study directory you will find
''rfx''               - second level analysis, if used[[BR]]

=== location of aa files ===
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 study

''done_[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.