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
_________________________________________
Nu Ri Choi
Undergraduate Student, Washington University in St. Louis
Computer Science + Math
Mobile: 314-327-2303
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