Derivatives

Folder Level 1 - Analysis Type

BIDS formatted derivatives follow the same organization format of our scripts.

Note how the folders in the derivatives folder above correspond to folders in the main scripts folder. This should be the same for all of our studies (IAM, PUSH, etc.) with the caveat that MRS and PET data are only present for IAM and no other studies. "Misc" folders can be added if a pipeline does not fall into any of the given major subfolders.

Folder Level 2 - Pipeline

Within each of these folders are more specific pipelines. These specific pipelines will vary from study to study because of differences in data collection, needs, aims, etc.

Generally, all studies should have the following derivative pipeline subfolders:

PyDesigner, Freesurfer 6.0 and 7.2, and LST are all pipelines we automatically run on all of our data. Note that some pipelines may have numerous "pydesigner" folders with prefixes like "FBI", "30dir", and "64dir". This will vary by study as well.

Folder Level 3 - Subjects and Timepoints

Within each pipeline folder will be a folder for each subject which will contain subfolders for each timepoint. This mirrors the way raw data is organized.

Folder Level 4 - Output Folders and Files

Within each sub-NNN/ses-YY folder should be outputs from the pipeline see in Folder Level 2