Hi Jiachen

the field inhomogeneity can't really be estimated with only one structure since it is a function of space. You could check the ratio of amygdala in intensity in the orig.mgz with other gray matter that is far away (e.g. motor cortex or calcarine), but there may be scaling differences in the orig that you will need to account for as well.

cheers Bruce

On Tue, 4 Jun 2019, chen wrote:

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Hi experts, I selected hippocampus and amygdala as ROIs to estimated the reliability of a well-controlled multi-site study. But, amygdala volume (generated by FreeSurfer) presented a relatively poor ICC scores between sites.  The major sources of between-site variation might be related to field inhomogeneity and other issues idiosyncratic to individual each scanners. Due to this reason, i want to check my data to confirm the field inhomogeneity located in amydala area or not.   How can i get the difference between the original image and the images after motion and NU intensity? I am looking forward to your suggests.

Cheers, Jiachen