Hi Yi Zheng:

I'm not from Conn team but here's my answer to your questions.

1. I think both FSL and Conn are registering into the same standard space so it's totally fine to do that. But since Conn also provide nifti files which include the networks(conn/rois/networks.nii) and atlas(conn/rois/atlas.nii), it would be safer to use that if the atlas you're trying to use is one of the atlases that you can see in Conn GUI.

2. Yes, I think it is.

3. You can find the ROI denoised time series in 'results/preprocessing/ROI_Subject*_Condition*.mat'.

One thing to be notice is that Conn combine multiple sessions time series into one in the newest version. So if you have more than one sessions, you need to extract the session you want manually. Here's a link that address this issue:  https://www.nitrc.org/forum/message.php?msg_id=13863

Hope it helps!

Best,
Yu