Dear FreeSurfer Community,

I am currently analyzing structural MRI data using FreeSurfer 8 and have a specific question regarding the longitudinal pipeline. My dataset consists of two groups:

• One group has 3 follow-up timepoints
  
• The other group has 2 follow-up timepoints

I have processed the data using both the cross-sectional and longitudinal recon-all pipelines, and I am now wondering whether it is appropriate to proceed with the longitudinal output, despite the unequal number of timepoints between groups.

Key Concerns:

1. Since FreeSurfer creates subject-specific within-subject templates, could the differing number of sessions lead to relevant systematic differences between the groups? Specifically, will the segmentation accuracy or signal-to-noise ratio be noticeably different between the groups due to these variations?
2. Would it be valid to continue using the longitudinal output but statistically account for the unequal number of sessions (e.g., via Linear Mixed Models)?
3. Alternatively, would it be preferable to use cross-sectional outputs to avoid potential biases introduced by differing template quality?
4. If I analyze only one specific timepoint for certain research questions, should I still use the longitudinal output, or would cross-sectional data be more appropriate?

I find myself torn between the improved segmentation accuracy of the longitudinal approach and the potential systematic differences introduced by the varying number of timepoints. Would a viable solution be to proceed with the longitudinal output while ensuring robustness by replicating key findings using cross-sectional data? 

I would greatly appreciate your insights on whether it is methodologically sound to proceed with the longitudinal pipeline in this case and, if so, how best to control for the unequal timepoints in statistical analysis.

Thank you very much for your time and guidance!

Best regards,

Lara