Thanks for your very helpful tutorial on registration! I'm going through it on some of my data now and excited to QC the results. 

I found the instructions for your antsreg_CC_deform_T1wstructural2MNI.sh script a little confusing in that in the example, it suggests to include the path of the moving image but doesn't explicitly say to include this in the $moving variable as well as the $dirIN variable. Since it took me a little time to troubleshoot what was going wrong I thought I'd mention it. It also seems like the $dirIN variable really doesn't need to be the path where the moving image is, which would be convenient to clarify.

In the meantime, for anyone else trying to troubleshoot this, if your errors are either related to basename: missing operand or any file that does not exist, the paths are likely your problem!

By the way, I think it would also be helpful to specify that FSL is required for this script in order to use the imglob functionality in the same command (I wasn't personally familiar with this function call!)

Thanks again for bringing so much great functionality to the toolbox!