The aseg.stats should be the same since that does not make reference to the surfaces. The aparc stats should have been different because the thickness should have been different. Can you check whether the thickness files are different?

On 10/8/18 9:39 AM, Jianzhong Chen wrote:

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Dear All,

I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the aseg stats and aparc stats with/without T2 are exactly the same. When I check the pial surfaces, I can see that they are very similar but not the same. So is it reasonable to see exactly the same stats?

An example of the pial surfaces with/without T2 is attached here. The red line is lh.pial with T2 and the yellow line is the lh.pial without T2

My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all -T2 T2.nii -T2pial -sd ${T2_dir}

My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii -all -sd ${T1_dir}

Thanks,

Jianzhong
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