Hello,
We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face .
To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help)
1) Step 1: mri_deface -i original_T1 -o deface_T1
2) Step 2: recon-all -i deface_T1
3) Step 3: recon-all -i original_T1 -deface
4) Step 4: recon-all -i original_T1
5) The results from Step 3 is exactly equal to Step 4
6) The results from Step 2 and Step3/4 have errors >20% in certain regions.
7) Step 1-4 are done with version 5.3.0
Any response will be greatly appreciated.
Thanks
Regards
Virendra
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