<> ---- ''' Contents ''' <> ---- = 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]'' <
> ''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 == 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<
> ''[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) images|| ||''realtime_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 format|| ||''results'' ||stores first level statistical model (if used)|| within the study directory you will find ||''rfx'' || second level analysis, if used|| === 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.