Hi, 

When working with the GUI you can locate your freesurfer brainmask.mgz for your structural images and conn then finds the associated surface images. I'm wondering if this works exactly the same way when using a batch script? Will setting batch.Setup.structurals{subn}='path/to/freesurfer/volume/subn'; result in the same type of behavior or is there an additional step needed?  

Thank you!