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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

Thanks for your help!

Best regards,
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