ECP MEG Data Folders

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At the MEG lab:

Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
RAW format.PNG
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work

All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
ECP Subject.PNG

Anatomy Layout

Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step 
ECP MEG Anatomy.png

Data Layout

RAW and tSSS

The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif 
RAW format.PNG


Initialization - Subject Dataframe

init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
AProject Folder.png

The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice The data file is stored in the row, and all of the documented processing steps are the columns Subject DataFrame.PNG

Initialization - Subject Processing Folders

init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
The _tsss.fif files are links to the tSSS folder.  If these folders are deleted, it will not affect the data in the tSSS folder
Process setup.png
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
The processing creates a folder called Process_*DataType*/Clean with the output of the baddata analysis
Clean data.png