I was wanting to know this as well. I couldn't get the conn scripts to work right. I found a different way by experimenting and is simple as heck. The reason I needed to change path names, is I updated my mac operating system. Never do that unless you really need to. My external hard drive is in NTFS, and whatever came with the hard drive didn't work on the new OS. After finding a free program, it would change the name of my hard drive to the programs own version of it. iBoysoft. 

Anyway, if you use conn, you also have spm. There is a function in spm called spm_changepath.m which I have used before for spm. In this example, I was just changing every file path that had my "hard drives" name with what this new plugin to write in NTFS was creating. This assumes you changed directory to your conn base folder:

spm_changepath('myconnproject.mat', 'Benson', 'iboysoft_ntfs_disk2s2_')

Being kind of like /Volumes/Benson/Imaging_data/....... to /Volumes/iboysoft_ntfs_disk2s2_/Imaging_data/.......

It might yell at you the first time saying it can't find some .....dmat file when you first open it. I think conn is assuming you want to merge files. Just close the error. It will work from there. I just wanted to change the ROI's used at the first level step, and worked perfect all the way through getting 2nd level results.

Many Blessings,
Benson