Hi Xiaowei
you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz
The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well
cheers Bruce
On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote:
Dear Freesurfer expert,
I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2.
Below are the details about the 2 images.
T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8)
T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).
The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly.
Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation?
Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output?
Any suggestion will help.
Sincerely thanks,
Xiaowei.
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Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health
Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051
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