I am working with a dataset that was acquired with oblique slices aligned to each participant's ac-pc line.

1) I've run a handful of subjects through mri_convert and the recon stream and each subject has a slight abnormality in the ventral temporal regions. It's subtle but apparent in each acquisition (image attached and the abnormality is apparent at the red cross). We believed it to be an alignment issue due to the oblique slices. Is there any way to fix this abnormality?

2) Are there any different preprocessing steps that should be added to mri_convert or the recon stream?

Thanks much in advance!

Kate