I think this was a bug in 5.3. Try running recon-all like
recon-all -s subject -parcstats -parcstats2 -parcstats3
to regenerate the stats files

On 10/09/2018 11:19 PM, Jianzhong Chen wrote:
>
>         External Email - Use Caution
>
> They are different. I attached two screenshots of lh.thickness
> overlaying on lh.inflated here.
>
> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu>> 于2018年10月9日周二 下午10:22写道：
>
>     But are the lh.thickness files the same or different?
>
>     On 10/9/18 1:46 AM, Jianzhong Chen wrote:
>>
>>             External Email - Use Caution
>>
>>     Hi Dr. Greve,
>>
>>     I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses
>>     (and the other measures like volume and area) are all the same.
>>
>>     Thanks,
>>     Jianzhong
>>
>>     Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>     <mailto:DGREVE@mgh.harvard.edu>> 于2018年10月9日周二 上午10:16写道：
>>
>>         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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