I am using the CONN toolbox to preprocess and denoise the MRI data of ABCD study. I am attaching the fMRI data that I obtained after preprocessing and denoising. This nifti data was converted from "DATA_SubjectXXX_Condition001.mat" under the folder /results/preprocessing. There are two problems that I can observe: (1) The signal did not normalize to percentage although I set it to percent signal change. (2) The upper part of the brain is missing. I observed other subjects can miss the back part of the brain. Could you please diagnose what kind of mistake I might make during the preprocessing or the denoising step?

During the procedure, I chose the default setup except for "slice order: do not know" during preprocessing and skipping scrubbing during denoising. Please note for each participant, I processed two fMRI scans. So CONN toolbox concatenated the two runs while processing them. I am not sure if this matters. Thanks for the help!