Hi David,

there is no need to worry. Whenever we change the pipeline, there will be consistent differences. Since we do not have ground truth thickness it is unclear which method is “more right”. A comparison between cross and long does not make sense here with respect to absolute values. It does make sense with respect to test-retest reliability and group differentiation sensitivity where long performs better.

However, as you noted and as we say in our tutorials, it is absolutely important to run single time point subjects through the longitudinal stream so that those images undergo the same processing steps as other images from subjects with more than 1 time point. That way the values are comparable again and can be included in the linear mixed effects analysis to estimate cross subject variances.

Simply run cross base with only one time point and long for all single time point subjects

Best, Martin

On 9. Nov 2018, at 15:04, Pagliaccio, David (NYSPI) David.Pagliaccio@nyspi.columbia.edu wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer