Hi Michelle,

when scanners (or even scanner hardware, like head coil or software upgrades etc) change in a longitudinal study you will have difficulties finding out whether the changes you see are real anatomical changes or scanner effects. This is true for any software pipeline (longitudinal or not). Often these changes are regional, not linear and not just offsets. Often the seem to interact with disease, age etc (meaning they affect older or more diseased subjects differently from young or healthy subjects). Therefore even including a co-variate to correct for scanner upgrade in the statistics may not be sufficient.

In your case you can either run the analysis only with the first three time points. Or run it with all three and include a scanner covariate in the statistic with interaction terms. In both cases you would profit from using the longitudinal stream in Freesurfer.

Best, Martin

Hello, 

Would it be ok to use the longitudinal pipeline for scans that were acquired on different scanners (e.g time 1 and time 2 on the same scanner, time 3 on different scanner)? Would the longitudinal pipeline help to account for different scanners, since it creates the average base image for all 3 time points? or is this not recommended?

Thank you,

Michelle 

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

mrv2115@columbia.edu

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