Processing Pipeline Dependencies

[joe_zhao]

Hello,

After reading the pre-processing pipeline configuration documentation of C-PAC (Pre- and post-processing - C-PAC 1.8.7.dev1 Beta documentation), I have questions about the dependencies of the pre-processing steps.

C-PAC provides six main processing steps:

1. • [Anatomical Preprocessing]
2. • [Functional Preprocessing]
3. • [Nuisance Corrections]
4. • [Timeseries Extraction]
5. • [Configuring ROI Time Series Extraction]
6. • [After Warp Settings]

My question is: Are the later steps dependent on the earlier ones? For instance, if I set run: Off for Anatomical Preprocessing, Functional Preprocessing, and Nuisance Corrections, would the Timeseries Extraction step produce the same output as it would if the earlier three steps were enabled?

[tamsinrogers]

Hi @joe_zhao,

The short answer to your question is generally yes - the later pre-processing steps are dependent on the earlier pre-processing steps.

There are some caveats, including a few places where the order is configurable (ACPC, motion stats, bandpass filtering) and that there likely exist a few combinations of steps that have no effect on each other.

It’s important to note that the “resources” used by C-PAC do get modified in the pre-processing steps (and then fed into future steps). In particular ,the desc-preproc_T1w and desc-preproc_bold will give different outputs depending on which steps are run in the pipeline.

Please let me know if you have any additional questions or I can clarify further!
-Tamsin