Hi John,

I do not have enough experience with pediatric samples so I am going to ask around to get a better answer (and other CONN users please feel free to chime in). My impression is that for this age-range the best choices are to either use an age-appropriate pediatric template or to use a group-specific template (e.g. using DARTEL or freesurfer), and that for any of these choices (unless you have a EPI-template) you would want to use "indirect normalization" (i.e. normalize your structural volumes and apply the same transformation to your already-coregistered functional data). 

Regarding the specifics of how to do this in CONN, if you would like to use your own age-appropriate template (I am going to assume here that you have a T1-template, but let me know if your template is defined differently), the simplest way to do this would be by using SPM8 instead of SPM12 (this is because the default normalization in SPM12 uses tissue probability maps instead of a T1 template). After importing your data into CONN, simply type the following command in Matlab's command window to run all preprocessing steps:

 conn_setup_preproc({'functional_realign&unwarp', 'functional_slicetime', 'functional_coregister', 'structural_segment&normalize', 'functional_art', 'functional_smooth'}, 'applytofunctional', true, 'structural_template', '/template.img');

(changing './template.img' to the location of your structural template file). That will run all standard preprocessing steps including the normalization to your own template (it is also possible to do the same using the GUI or using SPM12 but both of these options would require a somewhat more involved procedure).

Hope this helps and let me know if your template is defined differently and/or if you would like me to elaborate on some of the alternative options
Alfonso

EDIT: I corrected the conn_setup_preproc line above (added a missing argument)

Originally posted by John Hutton: