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FreeSurfer was originally developed on T1w as that gave the best G/W contrast; MPRAGEs were also pretty standard and higher res than the T2 when we developed. That said, it is possible to just reverse the contrast of the T2 to make it T1w and then run recon-all. We are actively developing multi-modal/modality independent surface placement.

On 9/23/2023 2:09 PM, Michael Mc Laughlin wrote:

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Hi,

I am curious to know why Freesurfer prefers a T1 weighted scan to a T2 weighted one.

Superficially at least, the T2 scan appears to have as good GM/WM contrast with the added benefit of being able to more easily distinguish CSF from bone. 

The above scans are from ERNIE test subject. The first one is T1 weighted and the second is T2 weighted.

Michael McLaughlin,

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