Thanks for your help, Alfonso.

I took a look at all of the 'check coregistration' options you suggested and couldn't find an issue.

As a work around I created a new project and used the Wizard to select data and have preprocessing go through Conn. This worked out well (no issues with coregistration when I got to denoising!) but now I have a new question: my images are all brains with stroke infarcts, some in the left hemisphere and some in the right. I would like to set up my Conn analysis so that all infarcts are in the left hemisphere (so rather than left side corresponding to left hemisphere, left side corresponds to ipsilesional hemisphere). Any suggestions on how to make this happen while still using the wizard? I can flip the necessary structural T1 images, but the corresponding functional images will not be flipped.

Thank you for your help,
Morgan