Hi Dani, 

the regular FreeSurfer stream samples everything to 1mm isotropic. This is of course problematic, if you have one group scanned at 1mm and the other at a different resolution (as group differences could be affected by the different resolutions). You would never know how much of what you get is group and how much is resolution. 

Similarly this is problematic if you switch scanner, software, head-coil, resolution in a longitudinal study. Effects cannot be separated any longer and all you can report in a paper is that what you find is longitudinal effect plus resolution effects and you don’t know how much is which. 

FreeSurfers longitudinal stream therefore requires inputs to be the same resolution. This safety feature (to prevent potentially meaningless analysis) can be circumvented by manually sampling images first - at your own risk. If you go that way, you should at least also interpolate the 1mm images to a new position (at least then both images will have interpolation artefacts, so that differences are only the acquisition resolution and not additionally interpolation artefacts in one of the time points). 

As an example, taking the same image twice, mapping one to a different location and back again produces interpolation artefacts that are significant and at orders comparable with 1 year of neurodegenerative disease. 

Best, Martin

On 30. Aug 2018, at 18:22, Daniel Ferreira <daniferp@gmail.com> wrote:

Dear colleagues,

I was wondering if resampling voxel size is done during recon-all.

Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be performed by any way) that minimizes these differences in somehow.

Thank you very much

Dani

--

Daniel Ferreira, PhD, Assistant Professor

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society

Karolinska Institutet (Sweden)

Address: Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla@ki.se

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