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Contents TableOfContents
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 isBR
[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) imagesBR 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 formatBR results - stores first level statistical model (if used)BR
within the study directory you will find rfx - second level analysis, if usedBR
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.