Step	Problem	Possible reason	Solution
1)	Orientation/resampling cannot be performed.	Non-raw images were provided.	We need images with correct header to extract the brain information (size, resolution, datatype, orientation, etc.). Use the raw images as the input and rerun the pipeline.
2)	Non-brain structures or the cerebellum are not well removed.	The brain image is scanned with too large obliquity or may contain large area of the shoulder structures.	1. Manually rotate the image to constrain the brain obliquity less than 30 degrees and then rerun the pipeline with the manually rotated image. 2. Crop the raw image to remove shoulder structures and then rerun the pipeline with the cropped image. 3. Manually edit the mask for the brain or the cerebellum generated from the pipeline with the interactive toolkit ITK-snap (http://www.itksnap.org), then rerun the pipeline by providing the corrected brain or cerebellum mask as additional input.
3)	The tissue segmentation map contains some errors.	The brain image is with severe motions.	1. If one modality was corrupted with severe motions while the other one was with free or moderate motions, run the pipeline with only the modality with free or moderate motions. 2. If only one modality is available but with severe motions, try to run the pipeline with downsampled modality (e.g., 1*1*1mm3). 3. Manually edit the segmentation map with the interactive toolkit ITK-snap (http://www.itksnap.org) and then rerun the pipeline using the corrected segmentation map as an additional input.
3)	Out of memory issue.	The GPU memory is too small.	1. Equip the GPU with at least 4GB memory. 2. Use our pipeline’s online version (www.ibeat.cloud) to conduct the processing.
6)	The reconstructed cortical surface has incorrect topology.	The topology correction may involve some errors.	Manually edit the left and right hemisphere tissue maps to remove topological errors.
6)	The reconstructed cortical surface is not aligned with the images.	The segmentation image has incorrect header.	Do not change the segmentation header when manually editing the segmentation map.