Hi,

I'm having trouble turning a gui job into a batch job correctly. In the GUI, whenever you add a structural image from freesurfer, it automatically asks if you want to import the aseg.mgz file and use the freesurfer defined gray matter, white matter, and csf masks as opposed to the SPM defined ones. I saw that i needed to use the conn_importaseg function, but I'm not sure where to list the resulting paths in the batch script to replicate the GUI options. Secondly, in the GUI, it automatically includes the effects of scrubbing and realignment as confounds in denoising as well, but this is not the case when using the batch script. Which options should I use and what file should I list to include these as confounds. I'm using v18.a if that helps at all. Hope to hear from you soon. Thanks

Edit: for reference I've attached 2 pictures of the denoising menu in the gui, one where the gui was used for processing and the other where a batch script was used for processing. I'm trying to get the batch to match the gui without actually needing to load it into the gui. I don't know if this is helpful or not, but just wanted to be clear.

-Matt