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I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version of FreeSurfer. I used cross-sectional pipeline to identify ROIs (from Desikan atlas) with significant difference in cortical volume (CV) between controls and *patients (subjects 1-40, baseline)*, say I get ROIs: R1, R2 and R3. I am using these ROIs (R1, R2 and R3) for further analysis to determine the effect of two treatments: *T1 (placebo) (for subjects 1 to 20) and T2 (active) (for subjects 21 to 40)*, compared to their corresponding baseline. I compared CV of these ROIs (R1, R2 and R3): *T1 vs. baseline and T2 vs. baseline* using both cross-sectional as well as longitudinal pipeline. *Using cross-sectional pipeline:* I found there is significant improvement in CV (p = 0.019) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. *Using longitudinal pipeline: *There is little improvement in CV (p = 0.2) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. I was wondering why I am getting results so different between these pipelines, and which pipeline suits better in such comparison when my ROIs are identified using cross-sectional pipeline, but further analysis of these ROIs involved longitudinal comparison. I would really appreciate any help (as early as possible). Thank you so much !
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