below I meant you could run it only on the first two time points. Maybe there is already enough power to see effects.

Best, Martin

Am 08.09.2017 um 09:13 schrieb Martin Reuter:

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

Am 05.09.2017 um 02:27 schrieb Michelle VanTieghem:

...

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 mailto:mrv2115@columbia.edu

---

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

---

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

The longitudinal pipeline will not overcome (contrast) differences due to scanner differences. If you register the scans to eachother you will see that there are slight differences in WM/GM contrast. Probably better to use the scans from the same scanner and not use the third.

Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Michelle VanTieghem Verzonden: zondag 17 september 2017 19:18 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] longitudinal freesurfer- different scanners

Hi all,

I just wanted to follow up on my question:

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 to use different scanners in longitudinal pipeline?

Thanks!

- M

On Mon, Sep 4, 2017 at 5:27 PM, Michelle VanTieghem michelle.vantieghem@gmail.com wrote:

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