I have a question about the input file of recon-all

I follow the tutorial, first use unpacksdcmdir to convert the original dcm file to a mgz file,then use the recon-all command with the mgz file as the input. I also tried to run the recon-all command with the original dcm file as the input. And I compare the output *.stats files with different inputs, the *.stats files I compared located in <subjectname>/stats/

Then I found a strange thing, the aseg.stats file between the two inputs is the same, however, the aparc file is different，and the difference in some index is larger than we thought.

So, I am not sure, which input file is OK for recon-all analysis?

I have attached the related results.

The version we use is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0

Thanks for your help!

ps1, we use siemens machine, so I put *.IMA as the dcm input

ps2, the scanning orient we use is sagittal, however, my partner has asked this question and was answered that we need't reorient it.

 

Sincerely, Jin