Hi Douglas,

Thank you so much for your replies. This is extremely helpful.

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, July 2, 2024 11:31:16 PM
Subject: Re: [Freesurfer] Scanner and Freesurfer-version differences

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Hi Freesurfer Mailing List,

I work on a large bipolar disorder imaging study that has been running for over 10 years. We previously acquired 2 sMRI time-points (pre 2013, n~500, n~250 at each time-point) on a single Philips 3T scanner and these images were processed with Freesurfer version 5.3. We have just now acquired a third imaging time-point that was completed on a different scanner (Siemans, n~120) using a different acquisition protocal. So I have three questions for the mailing list, that I'm hoping will inform the design of our analysis protocol:

1. Are there specific considerations for processing structural MRIs that have been acquired on different scanners and with different acquisition protocols?

No, we don't have anything special for this. Our experience is that the cortical results tend to be much less dependent upon the actual acquisition parameters and scanners.

1. Reprocessing all time 1 and time 2 images with a newer version of Freesurfer is a huge undertaking (for both processing time and personnel time required to review and edit). However, is there a reason why a newer version of Freesurfer should be used (e.g. publication considerations, more consistent output) as opposed to processing time 3 with v5.3?

I think you are ok to continue to use 5.3. Reviewers are pretty lenient about these kind of thing. Given the incremental longitudinal nature of the project, you can just switch and rerun everything.

1. I know there are differences in the output across different versions of Freesurfer. However, do different system set ups (e.g. linux, mac, as well as operating systems) have an impact on the output, even if the same version of Freesurfer is used?

You can get differences that are very small but systematic. If it is something you are worried about, treat the OS as another variable in the sense that you randomize the OS across your variables of interest (ie, don't have all your patients be from one OS and all your controls be from another). You could test the effect of OS; if it is not significant, you can remove it from the analysis.

Kind regards,

Bronwyn Overs

Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725

neura.edu.au 

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