On 4/24/2021 5:56 PM, AJ wrote:

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Hi,

Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?

I'll let Stefano (cc'ed) weigh in.

Can --eTIV be added to SAMSEG?

Not sure what you mean here. There is an etiv value that is output in the samseg folder

In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?

No, not yet

Can corpus callosum be segmented separately in Samseg?

I have not tried this, but you can try
mri_cc -aseg seg.mgz -o seg.cc.mgz

Sorry for all the questions.

Many thanks.

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