Dear CONN maintainers,

I have searched the forum (found especially this thread: https://www.nitrc.org/forum/message.php?... ), but I could not find answers to the following questions.

Background: I am running ROI-to-ROI, SBC analysis, and ICA. Some subjects have parts of the cerebellum missing due to an inappropriate FoV setting. Except for smoothing, the whole pre-processing was performed outside the CONN (e.g., normalized unsmoothed BOLD images were imported).

Questions:
1. How does CONN account for missing voxels when explicit mask is used? With explicit mask, the results viewer for SBC analysis still shows voxels in the cerebellum.
2. How is the implicit mask created? With implicit masking, cerebellum is (correctly) no longer visible in the results, but the resulting group brain mask contains non-brain tissue, such as the eyes and parts of the skull.
3. How does the explicit mask affect denoising? With the explicit mask, QC-FC associations indicate much worse performance (e.g., 88% match with NH compared to 97% match with NH when the implicit mask is used). Does the masking only affect the plots (since they also show voxels not covered by FoV) or does it influence the denoising procedure itself (e.g., by extracting CSF/WM signal from voxels where there are no data)?
4. Is there a way to force an intersection of implicit and explicit mask? That would probably solve all my issues.

Kind regards

Pavel Hok