There are several things you can try. First, you can use samseg instead of recon-all to generate the subcortical segmentation. Samseg works on any modality or combination of modalities. Second, you can try to build and apply your own atlas. This is more difficult, but you would start with gcatrain.

On 3/4/2021 10:26 PM, Choi, Nuri wrote:

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Hi,

I was wondering if it is possible for me to use FreeSurfer's subcortical segmentation feature with T2-weighted images. Our lab was hoping to make our own T2-weighted Aseg atlas (which I believe is possible with FreeSurfer) and run the subcortical segmentation using that atlas. However, since FreeSurfer is designed for T1-weighted images, I wasn't sure if it be possible to pass a T2w MRI image instead. We don't need any of the other features available from FreeSurfer, just the subcortical segmentation. Would doing this step for T2 MRI be feasible using FreeSurfer?

Thanks, -Nuri

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Nu Ri Choi

Undergraduate Student, Washington University in St. Louis

Computer Science + Math

Mobile: 314-327-2303

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