# 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 and the Summary Files folder. This should be the same for all of our studies (IAM, PUSH, etc.) with the caveat that certain data are only present for IAM and no other studies. ``` fMRI - any fMRI derived scripts/data Misc - any scripts/data which do not fit into other categories MRS - any MRS derives scripts/data PET - any PET derived scripts/data Preprocessing - pydesigner, freesurfer, and lst scripts/outputs Registration - any pipeline in which data was derived via a registration/normalization pipeline (DTI-TK, TBSS, etc.) Segmentations - any pipeline in which data was derived via a segmentation pipeline (native space ROI analyses, TractSeg) ViSTa - any ViSTa derived scripts/data ``` ## 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 --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization/derivatives.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.