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Hello Freesurfer gurus, We have two samples of approximately n~125-150 whose T1s were collected on the same scanner with the same acquisiton, except for a difference in head coil (8 vs 32 channel) and processed with different Freesurfer versions (v5.3.0 and v. 6.0.0). Both also had the FreeSurfer segmentation of hippocampal subfields v 6.0.0 applied. We would like your guidance about combining their data if possible to maximize sample size.
What would your suggestion be for hypothesis testing? Can we combine the samples - for example to test moderators of hippocampal x age relationships, using simply a covariate to account for the differences in acquisition/Freesurfer processing (in addition to the usual sociodemographic and estimated intracranial volume covariates)?
OR is that problematic and would you instead suggest keeping them separate and using one as a replication sample?
Thank you for your guidance! Stacey
Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project &
Co-Leader of the MIDUS Admin Core
MIDUS NEURO
Keystone House
901 University Bay Dr
Madison WI 53705
External Email - Use Caution
Resending in hopes of getting the experts' perspective! ________________________________ From: Stacey Schaefer Sent: Wednesday, September 10, 2025 10:21 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Question about combining data from cohorts processed with different Freesurfer versions
Hello Freesurfer gurus, We have two samples of approximately n~125-150 whose T1s were collected on the same scanner with the same acquisiton, except for a difference in head coil (8 vs 32 channel) and processed with different Freesurfer versions (v5.3.0 and v. 6.0.0). Both also had the FreeSurfer segmentation of hippocampal subfields v 6.0.0 applied. We would like your guidance about combining their data if possible to maximize sample size.
What would your suggestion be for hypothesis testing? Can we combine the samples - for example to test moderators of hippocampal x age relationships, using simply a covariate to account for the differences in acquisition/Freesurfer processing (in addition to the usual sociodemographic and estimated intracranial volume covariates)?
OR is that problematic and would you instead suggest keeping them separate and using one as a replication sample?
Thank you for your guidance! Stacey
Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project &
Co-Leader of the MIDUS Admin Core
MIDUS NEURO
Keystone House
901 University Bay Dr
Madison WI 53705
I think your approach of using a covariate will work well enough. The one thing you'll want to check is whether your statistical test will be confounded by headcoil/FSversion. Eg, if all your patients came from 8 channel and all your controls came from 32, then you would not know whether your differences are caused by diagnosis or by head coil.
On 9/10/2025 11:21 AM, Stacey Schaefer wrote:
External Email - Use Caution
Hello Freesurfer gurus, We have two samples of approximately n~125-150 whose T1s were collected on the same scanner with the same acquisiton, /except/ for a difference in head coil (8 vs 32 channel) and processed with different Freesurfer versions (v5.3.0 and v. 6.0.0). Both also had the FreeSurfer segmentation of hippocampal subfields v 6.0.0 applied. We would like your guidance about combining their data if possible to maximize sample size.
What would your suggestion be for hypothesis testing? Can we combine the samples - for example to test moderators of hippocampal x age relationships, using simply a covariate to account for the differences in acquisition/Freesurfer processing (in addition to the usual sociodemographic and estimated intracranial volume covariates)?
OR is that problematic and would you instead suggest keeping them separate and using one as a replication sample?
Thank you for your guidance! Stacey
*Stacey M. Schaefer, Ph.D.* Leader of the MIDUS Neuroscience Project &
Co-Leader of the MIDUS Admin Core
MIDUS NEURO
Keystone House
901 University Bay Dr
Madison WI 53705
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