I’m a trainee & fmri novice so I’d really appreciate any assistance!
My goal is to extract time series from an adolescent task-based scan for network analysis in R.
For fmriprep, I see that there is a pediatric MNI atlas I can use as the output space. However, I’m not sure how well this will work with other tools.
First, I was going to --use-syn-sdc for fieldmap-less distortion correction, but I believe I read this functions in a standard MNI atlas. If so, would this introduce some error?
Also, I’ve seen a previous suggestion to follow this tutorial to extract time series. However, I do not see the MNIpediatric atlas within nilearn’s database, only the standard MNI152. So, I’m not sure how well this approach would work with my adolescent dataset if I use the MNI-pediatric atlas in fmriprep.
A. Alternatively, I’ve had thoughts of using each subject’s T1 space as the output space, but I can’t seem to find a workflow I could follow to extract time series downstream if I did that.
B. Another thought I’ve had was using the fmridenoise tool and then extracting time series, but I’ve been warned about potentially re-introducing artifacts (https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.24528) if I use that approach.
Thank you for any advice!