Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
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----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
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
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