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Dear Freesurfer devs,

We are considering segmenting with the Freesurfer 6 dev version the hippocampus, the amygdala and the thalamus of several subjects who have already done the recon-all. Since we have a T1 image and T2 image with smaller voxel size, we have thought about using the *mode B: segmetation with an additional scan* as explained in the freesurfer webpage. In addition to voxel size, both images have slight differences in acquisition parameters. Taking into account this situation we have these questions:

- Since there are other slightly different parameters between image T1 and T2 in addition to voxel size (e.g. matrix size), it is correct to use B mode with additional scan or we should use multispectral segmentation?

- Is it necessary to make some previous modification on some image before running the script segment_HA.sh (e.g. coregister both images)?

- Is there a quality control that you can recommend after segmenting these structures?

Thanks for your help!

Best regards,