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:
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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,