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Hello, Our lab has been running a set of data from a pre/post-treatment study through the FreeSurfer v6 pipeline. I was comparing the pre-treatment structural values initially run through the cross-sectional pipeline with the same pre-treatment data later run through the longitudinal pipeline and was seeing the same issue as has been previously posted about (msg52994). Particularly, one cortical region of interest shows on average 0.24mm (8.8%) larger cortical thickness values processed in the longitudinal pipeline vs. the cross-sectional pipeline. While all participant’s data showed increased thickness in this area with the longitudinal vs. cross-sectional pipeline, this was not at all consistent across participants (ranging from 0.08 to 0.47mm differences [3-18%]). While the longitudinal pipeline would increase reliability and sensitivity comparing the pre to post-scans, we are just very concerned about these major and inconsistent differences analyzing the same baseline data with the different pipelines. Particularly, we have some attrition so most participants have 2 but some have only 1 scan and thus this feels like it could introduce systematic bias in overall thickness. Any input would be appreciated! David
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