AutomaticAnalysisFileStructure - MRC CBU Imaging Wiki

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Contents

Contents

  1. File Structure
    1. Raw data
    2. Processed data
      1. location of aa files

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.