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Depends on the data analysis that you want to do, the magnetic field strength between the two scanners may be a problem that affects the intensity distribution of the image overall that lead to under- or over-estimation. See, the following paper as an example of longitudinal studies.

https://secure-web.cisco.com/1kuKpr8oUx5I2iJ2rXAjhzY3dtnZ4sGJaDJBmg4nk6qbhDV...

Best, Ahmed, U of Kentucky

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reuter, Martin,Ph.D. MREUTER@mgh.harvard.edu Sent: Thursday, September 2, 2021 10:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all Longitudinal processing (baseline on 1.5T; followup on 3T)

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Hi Jay,

that would be possible, but we have no experience with such a setting.

The problem is that you will never know if any detected longitudinal change is due to the field strength/scanner/head coil chances or the changes in the way it is processed or real anatomical changes. This is why such a longitudinal study design is problematic. You could look at group differences (given that e.g. both groups are acquired/processed the same way and under the assumption that there is no interaction with group). However, the second assumption is probably not true, e.g. motion artefacts would be correlated with age and with disease and may affect downstream measurements differently across the two scanners.

Best, Martin

On 31. Aug 2021, at 11:15, Jayachandra Raghava jayachandra9978@gmail.com wrote:

Hello Experts,

I am planning to run the longitudinal processing pipeline (Freesurfer version 7.1.1). But I have a few subjects who were scanned on different scanner field strengths at baseline and followup.

For example :

Baseline was scanned on a 1.5T Siemens Scanner Followup was scanned on a 3.0T Siemes Trio Scanner

I am planning to

1. run the cross-sectional processing for baseline without the 3T flag
2. run the cross-sectional processing for followup with the 3T flag
3. then generate the unbiased template and longitudinally process all the time points without any special flags.

Is this the best way to process such data? Please let me know if there are any additional flags in the longitudinal processing pipeline to accommodate Scanner/Field strength changes.

Best wishes Jay

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