On 7/1/2024 1:05 AM, Bronwyn Overs wrote:
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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
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