Hi Martin, 

For your first question, it depends on if you expect structural changes to exist over time. If yes, in general, it may be better to use the averaged ("unbiased") T1 template.

However, I have read a longitudinal study in MCI that normalized both sessions with the T1 baseline template.

For the second question, in case you refer to data preprocessed by the CONN toolbox, yes, you can find the preprocessed data in the output folder. For instance, swau*.nii ---> smoothed, normalized, slice timing corrected, unwarped

Best regards,

Chih-Hao Lien

Originally posted by Martin Juneja:

Thank you so much Chih for sharing the previous discussion you had on this topic. Thats very helpful.

If I understood that correctly, I guess I can go ahead with using same baseline structural MRI images from session 1 in order to preprocess my two session resting-state fMRI data, correct? (rather than using structural images from corresponding sessions)

If so, I am assuming I can export the smoothed images for external analysis outside CONN, correct?

Any help would be greatly appreciated.

Best,
M