Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795